the film forum library tutorial contact

Occurrences of the word "Sockeye" in the Supplemental Comprehensive Analysis of the Federal Columbia River Power System by NOAA Fisheries FCRPS Biological Opinion, Supplemental Comprehensive Analysis, May 5, 2008

Taking into account the obstacles faced, the Prospective Actions provide
for the survival of the species with an adequate potential for recovery.

Chapter 8 Effects Analysis for Salmonids

Section 8.4 Snake River Sockeye Salmon

Species Overview Background

The Snake River (SR) sockeye salmon ESU includes all anadromous and residual sockeye from the Snake River basin, Idaho, as well as artificially propagated sockeye salmon from the Redfish Lake Captive Broodstock Program. Sockeye salmon were historically numerous in many areas of the Snake River basin prior to the European westward expansion. However, intense commercial harvest of sockeye along with other salmon species beginning in the mid- 1880s; the existence of Sunbeam Dam as a migration barrier between 1910 and the early 1930s; the eradication of sockeye from Sawtooth Valley lakes in the 1950s and 1960s; the development of mainstem hydropower projects on the lower Snake and Columbia Rivers in the 1970s and 1980s; and poor ocean conditions in 1977 through the late 1990s probably combined to reduce the stock to a very small remnant population. Snake River sockeye salmon are now found predominantly in a captive broodstock program associated with Redfish and the other Sawtooth Valley lakes. At the time of listing, one, one, and zero fish had returned to Redfish Lake in the three preceding years, respectively. The Snake River sockeye ESU was listed as endangered in 1991, reaffirmed in 2005.

The designated critical habitat for SR sockeye salmon includes all Columbia River estuarine areas and river reaches upstream to the confluence of the Columbia and Snake rivers; all Snake River reaches from the confluence of the Columbia River upstream to the confluence of the Salmon River; all Salmon River reaches from the confluence of the Snake River upstream to Alturas Lake Creek; Stanley, Redfish, Yellow Belly, Pettit, and Alturas lakes (including their inlet and outlet creeks); Alturas Lake Creek; and that portion of Valley Creek between Stanley and Lake Creek and the Salmon River.

Current Status & Recent Trends
This species has a very high risk of extinction. Between 1991 and 1998, all 16 of the natural- origin adult sockeye salmon that returned to the weir at Redfish Lake were incorporated into the captive broodstock program. The program has used multiple rearing sites to minimize chances of catastrophic loss of broodstock and has produced several hundred thousand eggs and juveniles, as well as several hundred adults, for release into the wild. Between 1999 and 2007, more that 355 adults returned from the ocean from captive broodstock releases -- almost 20 times the number of wild fish that returned in the 1990s. The program has been successful in its goals of preserving important lineages of Redfish Lake sockeye salmon for genetic variability and in preventing extinction in the near-term. The Stanley Basin Sockeye Technical Oversight Committee has determined that the next step toward meeting the goal of amplifying the wild population is to increase the number of smolts released.

Limiting Factors and Threats
By the time Snake River Sockeye were listed in 1991, the species had declined to the point that there was no longer a self-sustaining, naturally-spawning anadromous sockeye population. This has been the largest factor limiting the recovery of this ESU, important in terms of both risks due to catastrophic loss and potentially to genetic diversity. It is not yet clear whether the existing population retains sufficient genetic diversity to successfully adapt to the range of variable conditions that occur within its natural habitat. However, unpublished data from geneticists for the Stanley Basin Sockeye Technical Oversight Committee indicate that the captive broodstock has similar levels of haplotype diversity as other sockeye populations in the Pacific Northwest and that the program has been able to maintain rare alleles in the population over time. The broodstock program reduces the risk of domestication by using a spread-the-risk strategy, outplanting prespawning adults and fertilized eyed eggs as well as juveniles raised in the hatchery. The progeny of adults that spawn in the lakes and juveniles that hatch successfully from the eyed eggs are likely to have adapted to the lake environment rather than become "domesticated" to hatchery rearing conditions.

Recent Ocean and Mainstem Harvest
Few sockeye are caught in ocean fisheries. Ocean fishing mortality on Snake River Sockeye is assumed to be zero. Fisheries in the mainstem Columbia River that affect SR sockeye were managed subject to the terms of the U.S. v. Oregon Interim Management Agreement for 2005-2007. These fisheries were limited to ensure that the incidental take of ESA-listed SR sockeye does not exceed specified rates. Non-Treaty fisheries in the lower Columbia River were limited to a harvest rate of 1%. Treaty Indian fisheries are limited to a harvest rate of 5 to 7% depending on the run size of upriver sockeye stocks. Harvest rates have ranged from 0 to 0.95%, and 2.8 to 6.1% since 2001, respectively.

8.4.2 Current Rangewide Status
With this first step in the analysis, NOAA Fisheries accounts for the principal life history characteristics of each affected listed species. The starting point for this step is with the scientific analysis of species' status which forms the basis for the listing of the species as endangered or threatened.

8.4.2.1 Current Rangewide Status of the Species
The Snake River (SR) sockeye salmon ESU includes all anadromous and residual sockeye from the Snake River basin, Idaho, as well as artificially propagated sockeye salmon from the Redfish Lake Captive Broodstock Program (Table 8.4.2.1-1). Sockeye salmon were historically numerous in many areas of the Snake River basin prior to the European westward expansion. However, intense commercial harvest of sockeye along with other salmon species beginning in the mid-1880s; the existence of Sunbeam Dam as a migration barrier between 1910 and the early 1930s; the eradication of sockeye from Sawtooth Valley lakes in the 1950s and 1960s; the development of mainstem hydropower projects on the lower Snake and Columbia Rivers in the 1970s and 1980s; and poor ocean conditions in 1977 through the late 1990s probably combined to reduce the stock to a very small remnant population. Snake River sockeye salmon are now found predominantly in a captive broodstock program associated with Redfish and the other Sawtooth Valley lakes (NMFS 1991a). At the time of listing, one, one, and zero fish had returned to Redfish Lake in the three preceding years, respectively.

Waples et al. (1997) examined the genetics of 0. nerka from Sawtooth Valley lakes to determine whether the remnant population represented a distinct species or had been diluted by nonnative stocking during the 20th century. Sockeye salmon that returned to Redfish Lake during 1991 to 1993 were genetically distinct from Fishhook Creek kokanee, but were similar to juvenile sockeye outmigrants and a small group of "residual" sockeye salmon discovered in the lake in 1992.¹

¹ Residual sockeye salmon are progeny of anadromous or residual fish that remain in freshwater to mature and reproduce. They produce some anadromous offspring (Kline 1994). Residuals are genetically very similar to the anadromous for (Waples et al. 1997) and are ESA-listed along with the anadromous portion of the ESU.

Historically, adult SR sockeye salmon entered the Columbia River in June and July, migrated upstream through the Snake and Salmon rivers, and arrived at the Sawtooth Valley Lakes in August and September (Bjornn et al. 1968). Spawning in lakeshore gravels peaked in October. Fry emerged in late April and May and moved immediately to the open waters of the lake where they fed on plankton for one to three years before migrating to the ocean. Juvenile sockeye generally left the Sawtooth Valley Lakes from late April through May and migrated nearly 900 miles to the Pacific Ocean. While pre-dam reports indicate that sockeye salmon smolts migrated through the lower Snake River in May and June, PIT-tagged smolts from Redfish Lake recently passed Lower Granite Dam during mid-May to mid-July. Snake River sockeye spend two to three years in the ocean before returning to their natal lake to spawn.

Table 8.4.2.1-1. Snake River sockeye ESU description. (Sources: NMFS 2005a ; ICTRT 2003; McClure et al. 2005; and Flagg 2007)

ESU Description Endangered
Listed under ESA in 1991, reaffirmed in 2005
Population
Anadromous sockeye salmon in the Snake River basin and residual sockeye in Redfish Lake ²

² Progeny of Redfish Lake sockeye have been outplanted to Pettit and Alturas lakes. These fish and their descendants, including residual sockeye salmon in Pettit Lake, are also considered part of the ESU.

Limiting Factors
By the time Snake River Sockeye were listed in 1991, the species had declined to the point that there was no longer a self-sustaining, naturally-spawning sockeye population. The absence of a functional natural population is the largest factor limiting the recovery of this ESU, important in terms of both risks due to catastrophic loss and potentially to genetic diversity. The population size issue will be directly addressed by the proposed action, which will result in roughly a 10-fold increase in the smolt releases from the current captive broodstock hatchery program. The captive broodstock program has succeeded in maintaining generations of sockeye that are derived from the remnants of the Redfish Lake population. It is now capable of expanding the number of fish produced in subsequent generations and the proposed action will result in the release of up to 1 million smolts per year, a level sufficient to seed Redfish Lake with natural spawners. However, even if the number of natural spawners is much larger, genetic diversity could remain as a significant limiting factor. Before intervention, Snake River Sockeye reached such low numbers that there has been concern that genetic bottlenecks have resulted. It is not yet clear whether the existing population retains sufficient genetic diversity to successfully adapt to the range of variable conditions that occur within its natural habitat. However, unpublished data from geneticists for the Stanley Basin Sockeye Technical Oversight Committee indicate that the captive broodstock has similar levels of haplotype diversity as other sockeye populations in the Pacific Northwest and that the program has been able to maintain rare alleles in the population over time (Flagg 2008). The broodstock program reduces the risk of domestication by using a spread-the-risk strategy, outplanting prespawning adults and fertilized eyed eggs as well as juveniles raised in the hatchery. The progeny of adults that spawn in the lakes and juveniles that hatch successfully from the eyed eggs are likely to have adapted to the lake environment rather than become "domesticated" to hatchery rearing conditions.

Mainstem Hydro
Compared to Snake River spring/summer Chinook salmon, there is relatively little route-specific information on the survival of SR sockeye salmon through the FCRPS. Reach survival estimates are imprecise because sample sizes of migrants from the Snake River are small. Williams et al. (2005) used detections of all PIT-tagged sockeye smolts (2000-2003) to the tailrace at Lower Granite Dam for annual estimates of survival between Lower Granite and McNary dams. In 2003, the estimated survival of sockeye smolts was 72.5%, similar to that of yearling Chinook salmon, but in 2000 through 2002, sockeye survival was considerably lower (23.9% to 56.0%). The reason is unclear, but sockeye salmon juveniles appear to be prone to descaling. Williams et al. 2005 reported that between 1990 and 2001, two adults returned from 478 juveniles transported and only one adult returned from 3,925 PIT-tagged fish that migrated in-river (SARs of 0.4% vs. 0.03%, respectively). As with Chinook salmon, most untagged sockeye salmon smolts were transported to below Bonneville Dam. Nonetheless, few adult sockeye salmon returned to Lower Granite Dam in the last decade. The Prospective Action of using the hatchery to increase smolt releases will also increase sample sizes and allow better estimates of juvenile survival through the FCRPS.

Habitat
Chapman and Witty (1993) reviewed the human influences that have resulted in the low numbers of sockeye salmon. Irrigation dams extirpated the anadromous sockeye runs to Wallowa and Payette lakes. Although the residual form of sockeye remains, irrigation withdrawals from Alturas Lake Creek severely reduced the anadromous sockeye salmon population in the watershed in the early 1900s. Sunbeam Dam blocked fish passage on the upper mainstem Salmon River beginning in 1910. Though a fish ladder was built at the dam in 1919, passage remained unlikely until the early 1930s. The IDFG eliminated sockeye from Pettit, Yellow Belly, and Stanley lakes during 1955 to 1965 to manage recreational fisheries for trout. At the time of the initial listing (NMFS 1991a), the greatest habitat problem faced by the ESU was probably the lack of access to any of the lakes but Redfish. The fish barriers on Alturas and Pettit Lake creeks (an irrigation intake and a concrete rough fish barrier, respectively) were modified to facilitate passage of anadromous sockeye into these historical habitats in the early 1990s (Teuscher and Taki 1996, cited in Flagg et al. 2004). Although access to the spawning and rearing lakes is now considered functional, large portions of the migration corridor in the Salmon River (i.e., between Redfish Lake Creek and Yankee Fork Creek and between Thompson Creek and Squaw Creek) are water quality limited for temperature (IDEQ 2005), which is likely to reduce the survival of adult sockeye returning to the Stanley Basin in late July and August.

The USFS (USDA 2003) recommended the following site-specific measures to improve habitat conditions:

• Reduce lakeshore recreation pressure, particularly in shallow areas where sockeye spawn currently or historically
• Restore or maintain native vegetation that provides naturally resilient and productive shoreline habitats, through management of lakeside recreation and other human development
• Correct causes of listing Salmon River as water-quality limited (sediment and temperature) between the confluence of Redfish Lake Creek and that of Squaw Creek with the upper Salmon River.

• Mimic the shape and timing of the natural hydrograph in the mainstem Salmon River between the East Fork confluence and the headwaters

Harvest
Few sockeye are caught in ocean fisheries. Ocean fishing mortality on SR sockeye is assumed to be zero. Fisheries in the mainstem Columbia River that affect SR sockeye are currently managed subject to the terms of the U.S. v. Oregon Interim Management Agreement for 2005-2007. These fisheries are limited to ensure that the incidental take of ESA-listed SR sockeye does not exceed specified rates. Non-Indian fisheries in the lower Columbia River are limited to a harvest rate of 2%. Treaty Indian fisheries are limited to a harvest rate of 5 to 7%, depending on the run size of upriver sockeye stocks. Actual harvest rates have ranged from 0 to 1.8%, and 2.8 to 7.0%, respectively.

Current Status of the ESU
Between 1991 and 1998, all 16 of the natural-origin adult sockeye salmon that returned to the weir at Redfish Lake were incorporated into the captive broodstock program. The program has used multiple rearing sites to minimize chances of catastrophic loss of broodstock and has produced several hundred thousand eggs and juveniles, as well as several hundred adults, for release into the wild. Between 1999 and 2007, more than 355 adults returned from the ocean from captive broodstock releases - almost 20 times the number of wild fish that returned in the 1990s (Flagg et al. 2004).³

³ Some of these returning adults may have been anadromous progeny of residual sockeye.

8.4.2.2 Current Rangewide Status of Critical Habitat
Designated critical habitat for SR sockeye salmon includes all Columbia River estuarine areas and river reaches proceeding upstream to the confluence of the Columbia and Snake rivers; all Snake River reaches from the confluence of the Columbia River upstream to the confluence of the Salmon River; all Salmon River reaches from the confluence of the Snake River upstream to Alturas Lake Creek; Stanley, Redfish, Yellow Belly, Pettit, and Alturas lakes (including their inlet and outlet creeks); Alturas Lake Creek; and that portion of Valley Creek between Stanley Lake Creek and the Salmon River (NMFS 1993). The lower Columbia River corridor is among the areas of high conservation value to the ESU because it connects every population with the ocean and is used by rearing/migrating juveniles and migrating adults. The Columbia River estuary is a unique and essential area for juveniles and adults making the physiological transition between life in freshwater and marine habitats. Designated areas consist of the water, waterway bottom, and the adjacent riparian zone (defined as an area 300 feet from the normal high water line on each side of the river channel) (NMFS 1993). Designation did not involve rating the conservation value of specific watersheds as was done in subsequent designations (NMFS 2005b). The status of critical habitat is discussed further in Section 8.4.3.

8.4.3 Environmental Baseline
The following section evaluates the environmental baseline as the effects of past and ongoing human and natural factors within the action area. It includes the past and present impacts of all state, tribal, local, private, and other human activities in the action area, including impacts of these activities that will have occurred contemporaneously with this consultation. The effects of unrelated Federal actions affecting the same species or critical habitat that have completed formal or informal consultations are also part of the environmental baseline. For a detailed environmental baseline analysis pertinent to all species please see Chapter 5, Environmental Baseline, of the SCA.

8.4.3.1 Recent Hydro Operations and Configuration Improvements
Changes in hydrosystem operations and configuration that have been implemented since 1998 have improved in-river conditions for SR sockeye based on rates of descaling and mortality [see Figures B- 4 and B-5 in Martinson et al. 2007]. Changes have included the installation of surface bypass structures, minimum gap turbine runners, and spill deflectors; the relocation of bypass outfalls to avoid areas where predators collect; as well as other operational and structural changes (Appendix A in Corps et al. 2007b). Changes were designed to deflect fish from turbines and attract them to safer passage routes, increase the survival of juveniles that do use the turbine passage route, and reduce dissolved gas concentrations that might otherwise limit spill operations.

(bluefish recommends: Biological Effects of TDG Supersaturation by Army Corps of Engineers, Dissolved Gas Abatement Study, May 2002)

⁴ In 2007, the Chelan PUD released acoustic-tagged juvenile sockeye for evaluating the performance of its own systems. Because the ongoing passage study at McNary Dam uses the same technology, researchers obtained three- dimensional passage information (approach and passage behavior as well as fish passage and survival rates) for the fish marked by Chelan PUD. The USGS is currently working on these data and expects to publish preliminary findings by mid-summer (2008).

In addition to losses in the lower Columbia and Snake hydrosystem, both juvenile and adult sockeye are lost in the 462-mile migration corridor between Redfish Lake and Lower Granite Dam. Water withdrawals in the Upper Salmon River during juvenile migration are statistically related to decreased juvenile sockeye salmon survival through the reach (approximately a 20% reduction) (Arthaud et al. 2004). Of 614 adults that passed Lower Granite between 1999 and 2007, only 352 (57%) were recovered at Redfish Lake or the Sawtooth Hatchery weir (Kozakiewicz 2007). The factors responsible for these losses have not been established. However, the relatively large run size in 2000 provided an opportunity for a telemetry project to examine the migration behavior and survival of adult Snake River sockeye. Keefer et al. (2007) found that survival decreased as the season progressed and after July 13, none of the sockeye radio-tagged at Lower Granite Dam survived to the spawning grounds. The shift from relatively high survival of migrants that reached Lower Granite before mid-July to 100% loss coincided with the date that the Snake River at Anatone, Washington first reached 21 degrees C, indicating that elevated temperatures played an important role.

8.4.3.2 Recent Tributary Habitat Improvements
The Shoshone Bannock Tribes have been supplementing nitrogen and phosphorus and controlling non-native kokanee salmon competitors (i.e., for food resources) in the four Sawtooth Valley lakes (Redfish, Pettit, Alturas, and Stanley) since 1995. Based on water quality and biological sampling described in their annual reports (e.g., Kohler et al. 2007), these management strategies are increasing the carrying capacities of the lakes for rearing juvenile Snake River sockeye salmon. In part because Redfish and the other Sawtooth Valley lakes are naturally oligotrophic systems, nutrient supplementation has stimulated primary productivity and the development of a zooplankton community dominated by Daphnia spp. (Selbie et al. 2007). Juvenile O. nerka (anadromous and residualized sockeye) fed selectively on the large copepod Daphnia in Sawtooth Valley lakes during 2004 and 2006 (i.e., Daphnia made up a larger proportion of the diet than would be expected based on its availability in the water column), although the same pattern was not observed in 2005 (Kohler et al. 2005 and 2007, Taki et al. 2006). Also, limiting the number of female kokanee allowed to spawn in Redfish Lake has reduced grazing pressure on shared food resources.

8.4.3.3 Recent Estuary Habitat Improvements
For salmon that use a stream-type life-history strategy, restoration projects in the tidally influenced zone of the estuary between Bonneville Dam and approximately RM 40 are most likely to improve the functioning of the juvenile migration corridor. Projects that protect or restore riparian areas and breach or lower dikes and levees are likely to improve safe passage for this type of juvenile migrant. The FCRPS Action Agencies recently implemented 18 estuary habitat projects that removed passage barriers, providing access to good quality habitat (see Section 5.3.1.3 in Corps et al. 2007a).

8.4.3.4 Recent Predator Management Improvements

Avian Predation There are few quantitative data on rates of avian predation on SR sockeye salmon. Ryan et al. (2007) reported the numbers of PIT-tags from in-river juvenile migrants detected at Bonneville Dam and subsequently detected on estuarine bird colonies during 2006. Although the number of sockeye detected was very small compared to steelhead or Chinook, the study indicated that avian predators were consuming some Columbia basin (i.e., potentially Snake River) sockeye salmon. If so, then the Action Agencies' removal of the Caspian tern colony from Rice to East Sand Island in 1999 probably reduced predation rates on listed sockeye salmon to some small degree. PIT-tags from a few juvenile sockeye were also found on cormorant colonies in the estuary (Collis et al. 2001); this potential source of mortality has not been addressed.

Recently, Antolos et al. (2005) quantified predation on juvenile salmonids by Caspian terns nesting on Crescent Island (RM 316) in the mid-Columbia reach. Between 1,000 and 1,300 adult terns were associated with the colony during 2000 and 2001, respectively. These birds consumed approximately 465,000 juvenile salmonids in the first and approximately 679,000 in the second year. Based on PIT- tag recoveries at the colony, these were primarily steelhead from Upper Columbia River stocks. Less than 0.1% of the inriver migrating yearling Chinook from the Snake River and less than 1% of the yearling Chinook from the Upper Columbia were consumed. Presumably, a very small number of sockeye salmon, if any, were included in the "other salmonids" (i.e., not steelhead) category in the samples.

Piscivorous Fish Predation
Although predation of juvenile sockeye undoubtedly occurs, there is little direct evidence that piscivorous fish in the Columbia River consume juvenile sockeye salmon. Presumably, Zimmerman (1999) did not differentiate sockeye from "unidentified species" in the guts of pikeminnows, smallmouth bass, or walleye in the lower Snake and lower Columbia rivers because none or very few were identified. In contrast, Chinook were 29% of the prey of northern pikeminnows in lower Columbia reservoirs, 49% in the lower Snake River, and 64% downstream of Bonneville Dam. However, these observations are likely explained, in large part, by the fact that sockeye smolts make up a very small fraction of the overall number of migrating smolts (Ferguson 2006) in any given year.

8.4.3.5 Recent Hatchery Survival Improvements
The planting of fertilized eyed eggs and the release of prespawn adults for natural spawning has benefited the population through the production of unmarked smolts. Between 1991 and 1997, the number of unmarked smolts emigrating from Redfish Lake declined from levels in excess of 4,000 to only 300 individuals (IDFG 2006). No unmarked smolts were observed to emigrate from Pettit Lake until 1999, but since then, estimate that 23,000 unmarked smolts have done so. Approximately 26,000 unmarked smolts have emigrated from Redfish Lake since 1998. The IDFG estimates that in migration year 2005 alone, approximately 7,870 unmarked smolts out-migrated from Redfish Lake and 7,435 from Pettit Lake. The project sponsors are conducting genetic evaluations to confirm the origins of these fish, but hypothesize that most were derived from the prespawn adults released into Redfish Lake and the eyed-eggs planted in Pettit Lake.

8.4.3.6 Recent Harvest Rates
Non-Indian fisheries in the lower Columbia River are limited to a harvest rate of 1%. Treaty Indian fisheries are limited to a harvest rate of 5 to 7% depending on the run size of upriver sockeye stocks. Actual harvest rates over the last ten years have ranged from 0 to 0.9%, and 2.8 to 6.1%, respectively (TAC 2008, Table 15).

8.4.3.7 Status of Critical Habitat under the Environmental Baseline
A variety of human-caused and natural factors have contributed to the decline of SR sockeye salmon over the past century and have decreased the conservation value of essential features and PCEs of the species' designated critical habitat. Factors affecting the conservation value of critical habitat include passage barriers (especially high summer temperatures) in the mainstem lower Snake and Salmon rivers, passage mortality at the mainstem FCRPS dams, and high sediment loads in the upper reaches of the mainstem Salmon River. Factors affecting PCEs for spawning and rearing, juvenile and adult migration corridors are described below.

Spawning & Rearing Areas Most of the historical spawning and rearing areas in Redfish, Pettit, and Alturas lakes lie within nearly pristine areas where habitat conditions are considered functional.

Juvenile & Adult Migration Corridors
Juvenile sockeye migrate from the Sawtooth Valley lakes during late April through May. PIT-tagged smolts from Redfish Lake recently passed Lower Granite Dam during mid-May to mid-July. Adult SR sockeye salmon entered the Columbia River in June and July and migrated upstream through the Snake and Salmon rivers, arriving at Redfish Lake in August and September. Key factors limiting the functioning and conservation value of PCEs in juvenile and adult migration corridors (i.e., affecting safe passage) are:

• Juvenile and adult passage mortality [hydropower projects in the mainstem lower Snake and Columbia rivers]
• Juvenile and adult mortality in the lower Snake River above Lower Granite Dam and in the mainstem Salmon River [water withdrawals, temperature, and degraded riparian conditions]

8.4.3.8 Future Effects of Federal Actions with Completed Consultations
NOAA Fisheries searched its Public Consultation Tracking System Database (PCTS) for Federal actions occurring in the action area that had completed Section 7 consultations between December 1, 2004 and August 31, 2007 (i.e., updating this portion of the environmental baseline description in the 2004 FCRPS Biological Opinion) that have affected the status of the ESU and its designated critical habitat.

The USFS completed consultation on two projects -- the Valley Road Fire (emergency consultation) and Whitebark Pine treatment in the Redfish Lake Creek watershed. The Federal Highway Administration (FHWA)/Idaho Department of Transportation (IDT) consulted on repairs at Buckhorn Bridge (Salmon River Mile Post 184).

Projects in Lower Columbia River, Estuary, and Coastal Waters
Federal agencies also completed consultation on a large number of projects affecting habitat in the lower Columbia River including maintenance dredging and boat ramp/dock repairs, tar remediation at Tongue Point, bridge and road repairs, an embankment and riprap repair, and several habitat restoration projects that included stormwater facilities and programs. A total of five wave energy projects have been proposed for the Oregon coast and one for the Washington coast. NOAA Fisheries has completed consultation on one project, in Makah Bay on the Olympic Peninsula in Washington (NMFS 2007k).

NOAA Fisheries' Habitat Restoration Programs with Completed Consultations
NOAA Fisheries funds several large-scale habitat improvement programs that will affect the future status of the species considered in this SCA/Opinion and their designated critical habitat. These programs, which have undergone Section 7 consultation provide non-Federal partners with resources needed to accomplish statutory goals or, in the case of non-governmental organizations, to fulfill conservation objectives. Because projects often involve multiple parties using Federal funds, it can be difficult to distinguish between projects with a Federal nexus and those that can be properly described as Cumulative Effects. As a result, many of the projects submitted by the States of Washington, Oregon, and Idaho as Cumulative Effects actually received funding through the Pacific Coast Salmon Recovery Fund (NMFS 2007l), the Restoration Center Programs (NMFS 2004g), or the Mitchell Act-funded Irrigation Diversion Screening Program (NMFS 2000e). The objectives of these programs are described below, but to avoid "double counting," NOAA Fisheries considered the projects submitted by the states (see Chapter 17 in Corps et al. 2007a) as Cumulative Effects (Section 8.14.4).

Pacific Coastal Salmon Recovery Fund
Congress established the Pacific Coastal Salmon Recovery Fund (PCSRF) to contribute to the restoration and conservation of Pacific salmon and steelhead populations and their habitats. The states of Washington, Oregon, California, Idaho and Alaska, and the Pacific Coastal and Columbia River tribes receive Congressional PCSRF appropriations from NOAA Fisheries Service each year. The fund supplements existing state, tribal and local programs to foster development of federal-state-tribal-local partnerships in salmon and steelhead recovery and conservation. NOAA Fisheries has established memoranda of understanding (MOU) with the states of Washington, Oregon, California, Idaho and Alaska, and with three tribal commissions on behalf of 28 Indian tribes; Northwest Indian Fisheries Commission, Klamath River Inter- Tribal Fish & Water Commission, Columbia River Inter-Tribal Fish Commission. These MOUs establish criteria and processes for funding priority PCSRF projects. The PCSRF has made significant progress in achieving program goals, as indicated in Reports to Congress, workshops and independent reviews.

NOAA Restoration Center Programs NOAA Fisheries has consulted with itself on the activities of the NOAA Restoration Center in the Pacific Northwest. These include participation in the Damage Assessment and Restoration Program (DARP), Community-based Restoration Program (CRP), and Restoration Research Program. As part of the DARP, the RC participates in pursuing natural resource damage claims and uses the money collected to initiate restoration efforts. The CRP is a financial and technical assistance program which helps communities to implement habitat restoration projects. Projects are selected for funding in a competitive process based on their ecological benefits, technical merit, level of community involvement, and cost-effectiveness. National and regional partners and local organizations contribute matching funds, technical assistance, land, volunteer support or other in-kind services to help citizens carry out restoration.

Mitchell Act-funded Irrigation Diversion Screening Programs
Through annual cooperative agreements, NOAA Fisheries funds three states agencies to operate, maintain, and construct fish screening facilities at irrigation diversions and to operate and maintain adult fishways. The agreements are with Oregon Department of Fish and Wildlife, Idaho Department of Fish and Game, and Washington Department of Fish and Wildlife. The program also funds research, monitoring, evaluation, and maintenance of existing fishway structures, primarily those associated with diversions.

Summary

Effects on Species Status
The effects of the habitat restoration projects and tar remediation in the lower Columbia River on the viability of the species will be positive. Other projects, including Whitebark Pine treatment, bridge repairs, dock and boat launch construction, maintenance dredging, and embankment repair, will have neutral or short- or even long-term adverse effects. All of these actions have undergone section 7 consultation and were found to meet the ESA standards for avoiding jeopardy.

Effects on Critical Habitat
The future federal projects that restore habitat in the lower river will have positive effects on water quality. The other types of projects will have neutral or short- or even long-term adverse effects on safe passage and water quality. All of these actions have undergone section 7 consultation and were found to meet the ESA standards for avoiding any adverse modification of critical habitat.

These actions, including those that are likely to have adverse short-term or even long-term adverse effects, were found to meet the ESA standards for avoiding jeopardy and for avoiding any adverse modification of critical habitat.

8.4.4 Cumulative Effects Cumulative effects includes state, tribal, local, and private activities that are reasonably certain to occur within the action area and likely to affect the species. Their effects are considered qualitatively in this analysis.

As part of the Biological Opinion Collaboration process, the states of Oregon, Washington, and Idaho provided information on various ongoing and future or expected projects that NOAA Fisheries determined were reasonably certain to occur and will affect recovery efforts in the Interior Columbia Basin (see list of projects in Chapter 17 in Corps et al. 2007a). However, neither the State of Idaho nor NOAA Fisheries identified any habitat-related actions and programs by non-federal entities that were expected to benefit SR sockeye salmon.

Some types of human activities that contribute to cumulative effects are expected to have adverse impacts on populations and PCEs, many of which are activities that have occurred in the recent past and have been an effect of the environmental baseline. These can also be considered reasonably certain to occur in the future because they are currently ongoing or occurred frequently in the recent past, especially if authorizations or permits have not yet expired. Within the freshwater portion of the action area for the Prospective Actions, non-federal actions are likely to include water withdrawals (i.e., those pursuant to senior state water rights) and land use practices. In coastal waters within the action area, state, tribal, and local government actions are likely to be in the form of legislation, administrative rules, or policy initiatives, and fishing permits. Private activities are likely to be continuing commercial and sport fisheries and resource extraction, all of which can contaminate local or larger areas of the coastal ocean with hydrocarbon-based materials. Although these factors are ongoing to some extent and likely to continue in the future, past occurrence is not a guarantee of a continuing level of activity. That will depend on whether there are economic, administrative, and legal impediments (or in the case of contaminants, safeguards). Therefore, although NOAA Fisheries finds it likely that the cumulative effects of these activities will have adverse effects commensurate to those of similar past activities, it is not possible to quantify these effects.

8.4.5 Effects of the Prospective Actions
Continued operation of the FCRPS and Upper Snake projects, as well as the harvest action, will have continuing adverse effects that are described in this section. However, the FCRPS and Upper Snake Prospective Actions will ensure that these adverse effects are reduced from past levels. The Prospective Actions also include habitat improvement and predator reduction actions that are expected to be beneficial. Some habitat restoration and RM&E actions may have short- term, minor adverse effects, but these will be more than balanced by short- and long-term beneficial effects.

Continued funding of hatcheries by FCRPS Action Agencies will have both adverse and beneficial effects, as described in the SCA Hatchery Effects Appendix and in this section. The Prospective Actions will ensure continuation of the beneficial effects and will reduce any threats and adverse impacts posed by existing hatchery practices.

The effects of NOAA Fisheries' issuance of a Section 10 juvenile transportation permit on this species are included in the effects of the FCRPS, which is described in Section 8.4.5.1. See Chapter 10 of the FCRPS Biological Opinion for a discussion of this permit.

8.4.5.1 Effects of Hydro Operations & Configuration Prospective Actions
The Prospective Actions include a requirement that the Action Agencies assess the feasibility of using increased PIT-tagging for better estimates of juvenile smolt survival from Redfish Lake to Lower Granite Dam and through the mainstem FCRPS projects (RPA Action 52). This information is needed to optimize in-river passage and transport facilities for juvenile sockeye as well as for Chinook and steelhead. It will also help determine the specific actions that must be taken to address limiting factors in the mainstem Salmon River portion of the juvenile migration corridor.

Until better data are developed, NOAA Fisheries uses information developed for juvenile SR spring/summer Chinook as a surrogate for estimating the effects of the Prospective Actions in the mainstem migration corridor. Based on this information, the survival of juvenile sockeye is likely to increase with the implementation of surface passage routes at Little Goose, Lower Monumental, McNary and John Day dams in concert with training spill (amount and pattern) to provide safe egress (i.e., reduce delay and vulnerability to predators). Installing a long guide wall in The Dalles spillway tailrace will also improve egress conditions. Surface passage routes are designed to reduce juvenile travel time through the forebay of each project where predation rates are often the highest (Section 8.1.1.1). Additional benefits could pertain if faster migrating juveniles are in better condition (e.g., less stressed, greater energy reserves) upon reaching the Bonneville tailrace. Shifting the delivery of a portion of the USBR's flow augmentation water from summer to spring will slightly reduce travel time, susceptibility to predators, and stress.

Hydro Prospective Actions are likely to improve the survival of adult SR sockeye salmon between Bonneville and Lower Granite dams. These include improvements to the collection channel at The Dalles and to the ladders at John Day, McNary, Ice Harbor, Lower Monumental, and Lower Granite dams and other improvements in section 5.3.3.1 in Corps et al. (2007a). Because temperatures in the Salmon River during late July and August are probably contributing to the loss of adult sockeye between Lower Granite Dam and the Stanley Basin (Section 8.4.3.1), the Prospective Actions also require that the Action Agencies work with appropriate parties to investigate feasibility and potentially develop a plan for ground transport of adult sockeye through this reach. If feasible, transport would provide a short-term solution while specific habitat problems are identified and addressed.

Some of the configuration changes, discussed above, correspond to ISAB recommendations to proactively address the effects of climate change. As described in Section 8.1.3, the installation of surface passage routes and other configuration improvements that reduce delay and exposure to predators also reduce exposure to warm temperatures in project forebays. The regulation of outflow temperatures at Dworshak Dam will reduce summer water temperatures at Lower Granite, and to increasingly lesser extent, at Little Goose, Lower Monumental, and Ice Harbor dams.

Effects on Species Status
The survival of both juvenile and adult SR sockeye is expected to increase under the Prospective Actions due to improvements in the mainstem migration corridor, contributing to increased adult returns to the broodstock program and to the Sawtooth Valley lakes.

Effects on Critical Habitat
The hydro Prospective Actions are expected to increase the functioning of safe passage in the juvenile and adult migration corridors. To the extent that these improvements increase the number of adults returning to spawning areas, the hydro Prospective Actions could improve water quality and forage for juveniles by increasing the return of marine derived nutrients to spawning and rearing areas (Section 8.4.3.2)

8.4.5.2 Effects of Tributary Habitat Prospective Actions
The tributary habitat Prospective Actions do not include specific projects that will improve tributary habitat used by Snake River sockeye. However, the Action Agencies will undertake a study of possible sources and locations of mortality of juvenile sockeye before they reach the Snake River as described above (Section 8.4.5.1). As sockeye smolt production increases (Section 8.4.5.5), the Action Agencies will develop habitat projects to support natural production (Appendix B.2.2 in Corps et al. 2007b).

8.4.5.3 Effects of Estuary Prospective Actions
Juvenile sockeye rear in the natal lakes for one to three years before migrating to the ocean, a stream- type life history. Estuary habitat restoration projects implemented in the reach between Bonneville Dam and approximately RM40, restoring riparian function and access to the floodplain (see Section 5.3.3.3 in Corps et al. 2007a), are likely to improve the survival of juvenile Snake River sockeye.

Effects on Species Status
Restoration projects that are placed along the estuary corridor, with an emphasis on the upper portion of the estuary nearest to Bonneville Dam, are most likely to have a positive influence on life history diversity and spatial structure (Fresh et al 2005).

Effects on Critical Habitat
The Action Agencies have specified 14 projects to be implemented by 2009 that will improve the conservation value of the estuary as critical habitat for this species (section 5.3.3.3 in Corps et al. 2007a). These include restoring riparian function and access to tidal floodplains. Restoration actions in the estuary will have long-term beneficial effects at the project scale. Adverse effects to PCEs during construction are expected to be minor, occur only at the project scale, and persist for a short time.

8.4.5.4 Effects of Predation Prospective Actions Avian Predation
The Prospective Actions include relocating most of the Caspian terns to sites outside the Columbia basin (RPA Action 54). While this will be beneficial, the available evidence does not indicate that significant numbers of sockeye smolts have fallen prey to Caspian terns. Continued implementation and improvement of avian deterrence at mainstem dams (RPA Action 48) is also likely to increase juvenile sockeye survival by a small amount.

Piscivorous Fish Predation
There is little evidence that piscivorous fish in the Columbia basin prey on juvenile sockeye salmon (see discussion in Section 8.4.3.4). The best information currently available indicates that continued implementation of the base Northern Pikeminnow Management Program and continuation of the increased reward structure in the sport-reward fishery (RPA Action 43) is not likely to address a limiting factor for this species. Therefore, only a small increase in survival (safe passage in the juvenile migration corridor) is likely to result from decreased predation rates.

Effects on Species Status
The predation Prospective Actions are likely to have small positive effects on the survival of juvenile sockeye salmon.

Effects on Critical Habitat
Small positive effects on survival will correspond to a small improvement in the functioning of safe passage in the juvenile migration corridor.

8.4.5.5 Effects of Hatchery Prospective Actions
The Prospective Actions include two hatchery actions that are expected to benefit Snake River sockeye:

• Continue to fund the safety-net program to achieve the interim goal of annual releases of 150,000 smolts while also continuing to implement other release strategies in nursery lakes, such as fry and parr releases, eyed-egg incubation boxes, and adult releases for volitional spawning
• Fund further expansion of the sockeye program to increase total smolt releases to between 500,000 and 1 million fish

Effects on Species Status
The continuing and the expanded smolt releases are expected to result in an increase in the abundance and productivity of the naturally-spawning population.

Effects on Critical Habitat
The smolt releases are not expected to affect PCEs in designated critical habitat.

8.4.5.6 Effects of Harvest Prospective Actions
Management provisions for sockeye in the 2008 U.S. v. Oregon agreement have not changed from those in the prior agreement. Non-Indian fisheries in the lower Columbia River will be limited to a harvest rate of 1% and Treaty Indian fisheries to 5 to 7%, depending on the run size of upriver sockeye stocks (Table 8.4.5.6-1)

Table 8.4.5.6-1. Sockeye Harvest Rate Schedule.

River Mouth Sockeye Run Size	Treaty Harvest Rate	Non-Treaty Harvest Rate	Total Harvest Rate
< 50,000	5%	1%	6%
50,000 - 75,000	7%	1%	8%
> 75,000	7% *	1%	8% *

*If the upriver sockeye run size is projected to exceed 75,000 adults over Bonneville Dam, any party may propose harvest rates exceeding those specified in Part II.C.2. or Part II.C.3. of the 2008-2017 Management Agreement. The parties shall then prepare a revised biological assessment of proposed Columbia River fishery impacts on ESA-listed sockeye and shall submit it to NMFS for consultation under Section 7 of the ESA.

Effects on Species Status
The Prospective harvest rates will continue to have a small negative effect on the numbers of Snake River sockeye returning to the captive broodstock program and to spawn naturally in the Sawtooth Valley lakes.

Effects on Critical Habitat
The effects of harvest activities in the Prospective Actions on PCEs occur from boats or along the river banks, mostly in the mainstem Columbia River. The gear that are used include hook- and-line, drift and set gillnets, and hoop nets. These types of gear minimally disturb streambank vegetation or channel substrate. Effects on water quality are likely to be minor; these will be due to garbage or hazardous materials spilled from fishing boats or left on the banks. By removing adults that would otherwise return to spawning areas, harvest could affect water quality and forage for juveniles by decreasing the return of marine derived nutrients to spawning and rearing areas.

8.4.5.7 Research, Monitoring & Evaluation Prospective Actions
Please see Section 8.1.4 of this document.

8.4.6 Aggregate Effect of the Environmental Baseline, Prospective Actions, and Cumulative Effects on Snake River Sockeye
This section summarizes the basis for conclusions at the ESU level.

8.4.6.1 Recent Status of the Snake River Sockeye ESU & Critical Habitat
The Snake River sockeye salmon ESU is comprised of a single MPG and single population spawning and rearing in Redfish, Pettit, and Alturas lakes in the Sawtooth Valley, and includes artificially propagated sockeye salmon from the Redfish Lake Captive Broodstock Program. This population is the last remaining in a group of what were likely to have been independent populations occupying the Sawtooth Valley lakes. The Interior Columbia Basin TRT has designated this species at very high risk. The extremely low number of natural spawners and reliance on a captive Broodstock Program implemented in 1992 illustrates the high degree of risk faced by this population.

Recent annual abundances of natural-origin sockeye salmon to the Stanley Basin have been extremely low. Although residual sockeye salmon have been identified in Redfish and Pettit lakes, the abundance of the ESU is supported by adults produced through the captive propagation program. Recently, the smolt-to-adult survival of sockeye originating from the Sawtooth Valley lakes rarely has been greater than 0.3%. The current average productivity is substantially less than the productivity required for any population to be at Low (1-5%) long-term extinction risk at the minimum abundance threshold. Based on current abundance and productivity information, the Snake River sockeye salmon ESU does not meet the viability criteria for non-negligible risk of extinction over 100-year time period. Short-term extinction risk has been reduced by the captive propagation program; between 1999 and 2007, more than 355 adults returned from the ocean from captive broodstock releases - almost 20 times the number of wild fish that returned in the 1990s. The program has been successful in its goals of preserving important lineages of Redfish Lake sockeye salmon for genetic variability and in preventing extinction in the near-term.

Ocean fishing mortality on Snake River sockeye is assumed to be zero. Non-Indian fisheries in the lower Columbia River are limited to a harvest rate of 1%. Treaty Indian fisheries are limited to a harvest rate of 5 to 7% depending on the run size of upriver sockeye stocks. Actual harvest rates over the last ten years have ranged from 0 to 0.9%, and 2.8 to 6.1%, respectively.

A draft recovery plan containing strategies to address remaining key limiting factors is expected to be completed later in 2008. Given the extremely low levels of Snake River sockeye returns, initial recovery efforts are largely focused on improving survival rates of out-migrant smolts. The Stanley Basin Sockeye Technical Oversight Committee has determined that the next step toward meeting the goal of amplifying the wild population is to increase the number of smolts released.

The major factors limiting the conservation value of critical habitat for Snake River sockeye are the effects on the migration corridor posed by the mainstem lower Snake and Columbia River hydropower system, reduced tributary stream flows and high temperatures experienced by outmigrating smolts and returning adults, and barriers to tributary migration. The Sawtooth Valley lakes lie within nearly pristine areas. The production capacity of these naturally oligotrophic systems is low, but nutrient supplementation in recent years has stimulated primary productivity and the development of a favorable zooplankton forage community. Non-native kokanee salmon directly compete for zooplankton forage in most Sawtooth Valley lakes. Ocean conditions that have affected the status of this ESU generally have been poor since 1977, improving only in the last few years.

8.4.6.2 Effects of the Prospective Actions on Snake River Sockeye & Critical Habitat
Extinction of this ESU has been prevented and the prospects for survival and recovery now depend on expanding the existing safety-net program and increasing juvenile and adult survival. The Prospective Actions are expected to result in an approximately 10-fold increase in the number of sockeye produced by the captive broodstock program, greatly increasing the number of sockeye released to the wild, and thereby increasing the likelihood of higher adult returns. The Action Agencies will continue to fund the existing broodstock program including the continued releases of 150,000 fry and parr, outplanting of eyed-egg incubation boxes, and releases of adults for volitional spawning.

The Prospective Actions include configuration changes at FCRPS dams that are likely to improve the survival of juvenile and adult sockeye salmon, although more species-specific data are needed to ensure that conditions are optimized for this species as well as Chinook and steelhead. The Prospective Actions therefore require that the Action Agencies assess the feasibility of PIT-tag marking smolts for tracking survival of this species through the FCRPS. They will also work with appropriate parties to investigate feasibility and potentially develop a plan for ground transport of adult sockeye from Lower Granite Dam to Redfish Lake to circumvent the habitat problems that are causing losses until they can be addressed.

Management provisions for sockeye in the 2008 Agreement have not changed from those in the prior U.S. v. Oregon Agreement. Actual harvest rates over the last ten years have ranged from 0 to 0.9% for the non-Indian and 2.8 to 6.1% for the Treaty Indian fisheries, respectively (Section 8.4.3.6).

In aggregate, the prospective actions are expected to improve the survival of juveniles and adults through the mainstem Salmon and FCRPS migration corridors (safe passage) and together with the expanded smolt release program to increase the likelihood of higher adult returns.

8.4.6.3 Cumulative Effects Relevant to the Snake River Sockeye ESU
The State of Idaho did not identify any habitat-related actions and programs in the action area by non-Federal entities that are expected to address low flows and high temperature in the mainstem Salmon River. The cumulative effects of water withdrawals and land use practices that degrade riparian conditions are likely to continue the significant adverse effects of similar past activities that contributed to the environmental baseline for this ESU.

8.4.6.4 Effect of the Aggregate Environmental Baseline, Prospective Actions & Cumulative Effects on the Snake River Sockeye Salmon ESU
The aggregate effect of the environmental baseline, the Prospective Actions, and cumulative effects will be an improvement in the viability of SR sockeye salmon. Some limiting factors will be addressed by improvements to mainstem hydrosystem passage. The installation of surface passage routes and other configuration changes that will reduce delay and exposure to predators and warm temperatures in forebays, controlling summer water temperatures at Lower Granite by regulating outflow temperatures at Dworshak Dam, also correspond to ISAB recommendations to proactively address the effects of climate change (Section 8.1.3). However, based on an evaluation of future Federal actions that have completed Section 7 consultation and cumulative effects, conditions in the Salmon River portion of the juvenile and adult migration corridors are not expected to improve. If it is feasible to trap adults at Lower Granite Dam and haul them to the Sawtooth Valley, the adverse effects of low flows and high temperatures in the mainstem Salmon can be avoided, at least for this life stage. Management provisions for sockeye in the 2008 Agreement are unchanged from those in the prior U.S. v. Oregon Agreement and actual harvest rates are likely to be less than those allowed, as in previous years. Taking into account the obstacles faced, the Prospective Actions provide for the survival of the species with an adequate potential for recovery.

8.4.6.5 Effect of Aggregate Environmental Baseline, Prospective Actions & Cumulative Effects on PCEs of Critical Habitat
NOAA Fisheries designated critical habitat for SR sockeye salmon including all Columbia River estuarine areas and river reaches upstream to the confluence of the Columbia and Snake rivers; all Snake River reaches from the confluence of the Columbia River upstream to the confluence of the Salmon River; all Salmon River reaches from the confluence of the Snake River upstream to Alturas Lake Creek; Stanley, Redfish, Yellow Belly, Pettit, and Alturas lakes; Alturas Lake Creek; and that portion of Valley Creek between Stanley Lake Creek and the Salmon River. The environmental baseline within the action area, which encompasses these subbasins, has improved over the last decade but does not yet fully support the conservation value of designated critical habitat for SR sockeye salmon. The major factors currently limiting the conservation value of critical habitat are juvenile and adult mortality at mainstem hydro projects in the lower Snake and Columbia rivers and water withdrawals, temperature, and degraded riparian conditions in the lower Snake River above Lower Granite Dam, and in the mainstem Salmon River.

Although some current and historical effects of the existence and operation of the hydrosystem and tributary and estuarine land use will continue into the future, critical habitat will retain at least its current ability for PCEs to become functionally established and to serve its conservation role for the species in the near- and long-term. Prospective Actions will substantially improve the functioning of many of the PCEs; for example, implementation of surface passage routes at Little Goose, Lower Monumental, McNary, and John Day dams, in concert with training spill to provide safe egress (i.e., avoid predators) will improve safe passage in the juvenile migration corridor. Habitat work in the mainstem Salmon River and in the lower Columbia River and estuary will improve the functioning of water quality, natural cover/shelter, forage, riparian vegetation, space, and safe passage, restoring the conservation value of critical habitat at the project scale and sometimes in larger areas where benefits proliferate downstream. In addition, a number of actions in the mainstem migration corridor and in tributary and estuarine areas will proactively address the effects of climate change. These various improvements are sufficiently certain to occur and to be relied upon for this determination. They are either required by NOAA Fisheries' RPA for the FCRPS or otherwise the product of regional agreement and Action Agency commitment (Upper Snake actions are supported by the SRBA agreement and harvest by the 2008 U.S. v. Oregon Agreement). There are likely to be short-term, negative effects on some PCEs at the project scale during construction, but the positive effects will be long term. The species is expected to survive until these improvements are implemented, as described in "Short-term Extinction Risk," above.

Chapter 5 Environmental Baseline

5.1 Hydro System Effects
5.1.1 Blocked and Inundated Habitat
Before European contact, Snake River fall Chinook salmon occupied the mainstem Snake River up to Shoshone Falls (Gilbert and Evermann 1894; ICTRT 2003). In particular, the area downstream of Upper Salmon Falls, at river mile (RM) 578, was identified by Evermann (1895) as the "largest and most important salmon spawning ground of which we know in the Snake River." After loss of these upstream reaches with construction of Swan Falls Dam in 1901, the reach between Marsing, Idaho, and Swan Falls Dam (RM 349 to 424) was the primary spawning and rearing area for Snake River fall Chinook salmon (Irving and Bjornn 1981; Haas 1965, cited in ICTRT 2003). However, construction of the Hells Canyon Dam complex (1958-1967) cut off access to historical habitat upstream of RM 248. Additional fall Chinook habitat was lost through inundation as a result of the construction of the lower mainstem Snake River dams (Groves and Chandler 1999). In addition to the loss of fall Chinook salmon habitat on the mainstem Snake River, the Hells Canyon Dam complex cut off access to historical habitat in seven large tributaries for spring/summer Chinook salmon and steelhead. The seven tributaries are the Boise, Burnt, Malheur, Owyhee, Payette, Powder, and Weiser rivers (USBR 1997). Each of these tributaries provided hundreds of miles of spawning and rearing habitat for spring/summer Chinook salmon and steelhead (and several lakes for sockeye salmon in the Payette River basin) (Fulton 1968; Fulton 1970; Gustafson 1997).

Similarly, dams constructed in tributary streams often were constructed without fish passage facilities, or fish passage that was provided functioned poorly. For example, Sunbeam Dam, built in 1910 about 20 miles downstream from Redfish Lake on the main Salmon River, was too high for salmon to surmount by leaping and was originally constructed without fish passage facilities. Though a poorly functioning concrete fish ladder was completed in 1920 and the dam was breached by blasting in 1934, the relatively short life of Sunbeam Dam is considered to be a major contributor to the decline of Snake River sockeye. In similar ways, many tributaries have been blocked by dams lacking adequate fish passage facilities.

5.4.2.1 Effects of Temperature on Disease
Organism: Renibacterium salmoninarum
Disease: Bacterial Kidney Disease (BKD)
Temperature effects: Increased temperatures reduce infectivity, but increase the severity of infections (time until death) in laboratory trials.
Susceptible species: All salmonids, especially chinook and sockeye

5.5 Hatchery Effects
. . .
Hatchery programs have also been used as a tool to conserve the genetic resources of depressed natural populations and to reduce extinction risk, at least in the short-term (e.g. Snake River Sockeye). Such programs are designed to preserve the genetic resources that salmon and steelhead conservation depends on and buy time until the factors limiting salmon and steelhead viability are addressed. In this role, hatchery programs reduce the risk of extinction (NMFS 2005b). Hatchery programs that only conserve genetic resources, however, "do not substantially reduce the extinction risk of the ESU in the foreseeable future" or long-term (NMFS 2005b). Furthermore, hatchery programs that conserve vital genetic resources are not without risk because the manner in which these programs are implemented can affect the genetic structure and evolutionary trajectory of the target population by reducing genetic and phenotypic variability and patterns of local adaptation (ICTRT 2007b).

Table 5.6-1. Incidental take limits and expected incidental take (as proportion of total run size) of listed salmonids for non-Indian and treaty Indian fisheries under the 2005-07 Interim Management Agreement (table and associated footnotes taken from the Biological Opinion on the Interim Agreement (U.S. District Court 2005)).

ESU: Snake River Sockeye
Take Limits: 6.0 - 8.08 %
Treaty Indian: 2.8 - 7.0
Non-Indian: 0.0 - 1.0

Chapter 7 Analytical Methods for Salmonids

Interior Columbia River species without data sufficient to evaluate relevant quantitative metrics:

• Snake River Sockeye

Abundance and Productivity
Snake River sockeye salmon are at very low abundance levels with current returns originating from a captive rearing program. As a result of the virtual absence of naturally produced returns in recent years, specific quantitative estimates of trend and productivity of that component of the ESU are not currently feasible. Qualitative characterizations of abundance and productivity are apparent just from inspection of available information.

7.2.1.2 Analysis for Juvenile Migrants of Other ESUs
For the Lower Columbia and Willamette ESUs and for Snake River Sockeye, for which existing information is not sufficient for quantitative analysis of hydropower system effects, NOAA Fisheries must rely on a more qualitative approach.

The first approach uses ...

The second approach relies on providing professional judgment to qualitatively assess the likely effect of the FCRPS hydro actions on the ESUs for which empirical information is insufficient to provide useful quantitative assessments (SR fall Chinook salmon, SR sockeye, and CR chum). In this case, NOAA Fisheries considers the qualitative assessment made by the FCRPS Action Agencies in the CA and also any other information that would aid in the assessment of how these species are currently affected by the FCRPS and their likely response to the hydro actions required by the FCRPS RPA.

7.2.1.3 Methods for Adult Migrants of All ESUs
Recent survival of adult salmon and steelhead migrating through the FCRPS was assessed to identify ESU specific adult performance standards (and to estimate incidental take). NOAA Fisheries and the FCRPS Action Agencies, in collaboration with the Policy Work Group, adopted a methodology that removes the influence of several confounding variables (harvest and "natural" or transportation related stray rates)5 that obscure the true effect of the mainstem FCRPS dams on the survival of migrating adults. The assessment is based on returning adults6 detected at Bonneville Dam and redetected upstream at McNary dam or Lower Granite Dam (depending upon the ESU in question). Only returning adults of known origin, PIT-tagged as juveniles that migrated in-river to below Bonneville were included in the analysis to correct for the confounding variables identified above. See BA Section 2.1.2.2, Appendix B.2.6-2, and SCA Adult Survival Estimate Appendix for a more detailed description of this methodology.

This methodology is also used to develop standards for adult steelhead, recognizing the limitations/uncertainties of the harvest rate information available at this time. Similarly, this methodology is applied to the available information for Lake Wenatchee and Okanogan River sockeye salmon as a surrogate for adult Snake River sockeye survival. In this analysis, NOAA Fisheries qualitatively assesses the likely survival and effects of the Prospective Actions on migrating adults from these ESUs.

7.3 Methods for Considering Population Level Analysis at ESU/DPS level
. . .
The degree to which each population and MPG is individually analyzed varies with the species, due to varying amounts of relevant information as described in previous sections. In general, this process has resulted in more detail for most interior Columbia populations than for lower Columbia populations and Snake River sockeye salmon due to available information and degree of the impact of the FCRPS on the populations.

Chapter 9 Southern Resident Killer Whales

. . .
Southern Resident killer whales are known to consume 22 species of fish and one species of squid (Scheffer and Slipp 1948, Ford et al. 1998, 2000, Ford and Ellis 2006, Saulitis et al. 2000). A long-term study of resident killer whale diet identified salmon as their preferred prey (97 percent of prey consumed during spring, summer and fall) (Ford and Ellis 2006). Feeding records for Southern Residents suggest that diet resembles that of the Northern Residents, with a strong preference for Chinook salmon (78 percent of identified prey) during late spring to fall (Hanson et al. 2005, Ford and Ellis 2006). Chum salmon (11 percent) are also taken in significant amounts, especially in autumn. Other species eaten include coho (5 percent), steelhead (O. mykiss, 2 percent), sockeye (O. nerka, 1 percent), and non salmonids (e.g., Pacific herring and quillback rockfish [Sebastes maliger] 3 percent combined). Chinook were preferred despite the much lower abundance of Chinook in the study area in comparison to other salmonids (such as sockeye), presumably because of the species' large size, high fat and energy content, and year-round occurrence in the area. Killer whales also captured older (i.e., larger) than average Chinook (Ford and Ellis 2006).

Chapter 12 Literature Cited

Bjornn, T., D. Craddock, and D. Corley. 1968. Migration and survival of Redfish Lake, Idaho, sockeye salmon, Oncorhynchus nerka. Transactions of the American Fisheries Society. 97(4):360- 373.

Bjornn, T., D. Craddock, and D. Corley. 1968. Migration and survival of Redfish Lake, Idaho, sockeye salmon, Oncorhynchus nerka. Transactions of the American Fisheries Society. 97(4):360- 373.

Corps (U.S. Army Corps of Engineers). 2006a. Application for a permit to enhance the survival of listed species under the Endangered Species Act of 1973 for the purpose of a juvenile transportation program to protect sockeye, Chinook, and coho salmon, and steelhead from adverse environmental conditions created by Corps dams and reservoirs on the lower Snake and Columbia Rivers. Corps, Portland, Oregon.

Flagg, T.A., W.C. McAuley, P.A. Kline, M.S. Powell, D. Taki, and J.C. Gislason. 2004. Application of captive broodstocks to preservation of ESA-listed stocks of Pacific Salmon: Redfish Lake sockeye salmon case example. Pages 387-400 in M.J. Nickum, P.M. Mazik, J.G. Nickum, and D.D. MacKinlay, editors. Propagated fish in resource management. American Fisheries Society, Symposium 44, American Fisheries Society, Bethesda, Maryland.

Flagg, T.A. 2007. Snake River sockeye hatchery program. Communication to L. Krasnow, National Marine Fisheries Service from T.A. Flagg, National Marine Fisheries Service, Northwest Fisheries Science Center, Seattle, Washington. September 14.

Flagg, T.A. 2008. Snake River sockeye - genetic diversity. Communication to L. Krasnow, National Marine Fisheries Service, from T.A. Flagg, National Marine Fisheries Service, Northwest Fisheries Science Center, Seattle, Washington. April 3.

Fulton, L.A. 1970. Spawning areas and abundance of steelhead trout and coho, sockeye, and chum salmon in the Columbia river basin - past and present. Special scientific report, Fisheries No. 618. National Marine Fisheries Service, Washington, D.C.

Gustafson, R.G., T. Wainwright, G. Winans, F. Waknitz, L. Parker, and R. Waples. 1997. Status review of sockeye salmon from Washington and Oregon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-33, 282 p.

Gustafson, R.G., T. Wainwright, G. Winans, F. Waknitz, L. Parker, and R. Waples. 1997. Status review of sockeye salmon from Washington and Oregon. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-33, 282 p.

ICTRT (Interior Columbia Technical Recovery Team). 2003. Independent populations of Chinook, steelhead, and sockeye for listed Evolutionarily Significant Units within the interior Columbia River domain. Working draft.

IDFG (Idaho Department of Fish and Game). 2006. Project sponsor's (IDFG) response to ISRP review of proposal 199107200: Redfish Lake Sockeye Salmon Captive Broodstock Program. Submitted for fiscal years 2007-2009 funding through the Columbia River Fish and Wildlife Program. Columbia Basin Fish and Wildlife Authority, Portland, Oregon.

Keefer, M.L., C.A. Peery, and M.J. Heinrich. 2007. Temperature-mediated en route migration mortality and travel rates of endangered Snake River sockeye salmon. Ecology of Freshwater Fish, OnlineEarly Articles.

Kline, P. 1994. Research and recovery of Snake River sockeye salmon. Annual report 1993. Idaho Department of Fish and Game, Nampa.

Kohler, A.E., D. Taki, and R.G. Griswold. 2005. Snake River sockeye salmon habitat and limnological research. 2004 annual progress report. Prepared for Bonneville Power Administration, Portland, Oregon.

Kohler, A.E., J.L. Myers, R.G. Griswold, D. Taki. 2007. Snake River sockeye salmon habitat and limnological research. 2006 annual progress report. Prepared for Bonneville Power Administration, Portland, Oregon.

Kozakiewicz, V. 2007. Snake River sockeye returns. Communication to L. Krasnow, National Marine Fisheries Service from V. Kozakiewicz, National Marine Fisheries Service, Regional Office, Boise, Idaho. September 17.

NMFS (National Marine Fisheries Service). 1993. Designated critical habitat; Snake River sockeye salmon, Snake River spring/summer Chinook salmon, and Snake River fall Chinook salmon. Final rule. Federal Register 58:247(28 December 1993):68543-68554.

NMFS (National Marine Fisheries Service). 2001b. Endangered Species Act - Section 7 Consultation Biological Opinion on impacts of the interim management agreement for upriver spring Chinook, summer Chinook, and sockeye on salmon and steelhead listed under the Endangered Species Act. NMFS, Portland, Oregon.

Peterman, R.M. 1984. Density-dependent growth in early ocean life of sockeye salmon (Oncorhynchus nerka). Canadian Journal of Fisheries and Aquatic Sciences 41:1825- 1829.

Ruggerone, G.T., M. Zimmerman, K.W. Myers, J.L. Nielsen, and D.E. Rogers. 2003. Competition between Asian pink salmon (Oncorhynchus gorbuscha) and Alaskan sockeye salmon (O. nerka) in the North Pacific Ocean. Fisheries Oceanography 12(3):209-219.

Selbie, D.T., B.A. Lewis, J.P. Smol, and B.P. Finney. 2007. Long-term population dynamics of the endangered sockeye salmon: evidence of past influences on stock decline and impediments to recovery. Transactions of the American Fisheries Society 136:800-821.

Steig, T.W., J.W. Horchik, G.W. Tritt, J.R. Skalski, and R. Ngouenet. 2003. Comparison of PIT tagged and acoustic tagged juvenile Chinook, steelhead, and sockeye salmon passing Rocky Reach Dam in 2002. Final report to Chelan County Public Utility District No.1, by Hydroacoustic Technology, Seattle, Washington.

Steig, T.W., P.A. Nealson, K.K. Kumagai, B.J. Rowdon, L.S. Klein, and B.D. McFadden. 2007. Route specific passage of juvenile steelhead and sockeye salmon using acoustic tag methodologies at Rocky Reach and Rock Island Dams in 2006. Final report for Chelan County Public Utility District No. 1, by Hydroacoustic Technology, Seattle, Washington.

Steig, T.W., P.A. Nealson, K.K. Kumagai, J.W. Horchik, J.C. Sweet, and C.P. Mott. 2006a. Route specific passage of juvenile steelhead, Chinook, and sockeye salmon using acoustic tag methodologies at Rocky Reach and Rock Island Dams in 2004. Final report to Chelan County Public Utility District No.1, by Hydroacoustic Technology, Seattle, Washington.

Steig, T.W., P.A. Nealson, K.K. Kumagai, L.S. Brown, G.W. Tritt, K.C. Molitor, J.W. Horchik, M.A. Timko, J.C. Sweet, and C.P. Mott. 2006b. Route specific passage of juvenile steelhead, Chinook, and sockeye salmon using acoustic tag methodologies at Rocky Reach and Rock Island Dams in 2005. Final Report to Chelan County Public Utility District No.1, by Hydroacoustic Technology, Seattle, Washington.

Taki, D., A.E. Kohler, R.G. Griswold, and K. Gilliland. 2006. Snake River sockeye salmon habitat and limnological research: 2005 annual progress report. Prepared for Bonneville Power Administration, Portland, Oregon.

Timko, M.A., L.S. Brown, C.D. Wright, R.R. O'Connor, C.A. Fitzgerald, M.L. Meager, S.E. Rizor, P.A. Nealson, and S.V. Johnston. 2007. Analysis of juvenile Chinook, steelhead, and sockeye salmon behavior using acoustic tags at Wanapum and Priest Rapids Dams, 2006. Final report for Public Utility District No. 2 of Grant County, by Hydroacoustic Technology, Seattle, Washington.

US District Court (D. Oregon). 2005. US v. Oregon. Civil No. 68-513KI. 2005-2007 interim management agreement for upriver Chinook, sockeye, steelhead, coho and white sturgeon. May 11.

Related Pages:
Issue 19: Comments on Snake River Sockeye by NOAA Fisheries, FCRPS Biological Opinion, May 5, 2008
Biological Effects of TDG Supersaturation by Army Corps of Engineers, Dissolved Gas Abatement Study, May 2002