Lyons Ferry Hatchery Evaluation Fall Chinook Salmon Annual Report: 2001 and 2002

This report summarizes activities by the Washington Department of Fish and Wildlife's (WDFW) Lower Snake River Hatchery Evaluation Program from April 16, 2001 to April 15, 2003. Fall chinook salmon broodstock were obtained from the Lyons Ferry Hatchery (LFH) ladder and fish trapped and transported to LFH from Lower Granite (LGR) Dam. Only codedwire tagged (CWT), blank wire tagged (BWT), or ventral fin clipped salmon were collected at LGR Dam and transported to the hatchery.

The total number of fall chinook processed at spawning in 2001 was 5,977 fish (2,281 adults and jacks trapped at LFH and 3,696 adults and jacks trapped at LGR). Realizing there were more fish trapped than needed for broodstock, 727 of the fish on hand (52 fish trapped at LFH and 675 fish trapped at LGR Dam) were returned to the Snake River. Similar to 2002, the total number of fish processed during the season was 4,517 fish (2,728 adults and jacks trapped at LFH and 2,789 adults and jacks trapped at LGR Dam). Anticipating a large run it was decided to reduce the numbers of fish on hand to allow for sampling throughout the run. Because of this, 992 fish (501 trapped at LFH and 491 trapped at LGR Dam) were hauled back to the Snake River in 2002.

Fall chinook were spawned at LFH from October 23 to November 27, 2001 and from October 23 to November 25, 2002. Peak of spawning was November 13 and 14 in 2001 and November 12 and 13 in 2002. Coded-wire tags were removed from hatchery fish and read to determine the fish’s origin prior to mixing of gametes, unless they were Visible Implant Elastomer (VIE) tagged fish. Left red VIE fish that were used in broodstock were sub-sampled for CWT composition. Matings consisted of single female/single male lots with a backup male in 2001 while in 2002 backup males were not used. Only salmon verified to be of LFH/Snake River origin were used for broodstock.

To determine the composition of the run at LGR Dam as well as the run to LFH we read 59%- 100% of the VIE-CWT, CWT only, and AD-CWT groups. In 2001, any hatchery strays or unmarked fish were considered strays and removed from the population. This changed in 2002 when unmarked/untagged fish were released back into the Snake River. NOAA Fisheries allowed the return of these fish to the Snake River to continue their upward migration, based upon the assumption that these fish were primarily from upstream releases of unmarked LFH/Snake River hatchery origin fish. As in 2001, any stray fish were removed from the population since they were not needed elsewhere.

Sex, age, and mean length information was compiled for LFH/Snake River origin fall chinook salmon adults and jacks. These returns continued to be dominated by younger age class males. Females dominated the older age class of returning LFH/Snake River origin salmon because few males return at age-5 or older.

In 2001 and 2002, egg take from LFH/Snake River origin broodstock, prior to any transfers, was 4,734,234 and 4,910,467 green eggs, respectively. As a precaution, 144,530 and 44,900 green eggs from LFH/Snake River origin females which tested ELISA positive for Bacterial Kidney Disease were destroyed prior to eye-up in 2001 and 2002. This left 4,589,704 and 4,865,567 green eggs available for production in 2001 and 2002. Green egg to eye-up loss was estimated at 3.5% and 3.1% for the two years, excluding the eggs that were destroyed because of high ELISA titers.

In 2001 we transferred 200,064 eyed eggs (2001 brood) to Idaho Fish and Game (IDFG) for the Idaho Power Company mitigation agreement. The estimated number of LFH/Snake River origin fry ponded was 4,103,521 fish (2001 brood). In 2002 we shipped 616,000 green eggs (2002 brood) to Nez Perce Tribal Hatchery (NPTH) to help supplement their new hatchery. In addition, we transferred 7,000 green eggs to USFWS for research. After eye-up we transferred 230,000 eggs to IDFG, and another 336,967 fish to ODFW as part of the Idaho Power Company mitigation agreement. Also in 2002 5,100-eyed eggs (2002 brood) were transferred to Battelle Northwest Laboratories for research purposes. An estimated 3,481,685 fish (2002 brood) LFH/Snake River origin fry were ponded.

In 2001, to maximize survival of subyearlings released during a low flow/no spill year, LFH production subyearlings originally slated for onstation releases were barged to below Bonneville Dam. On June 1, 2001, we released 199,976 subyearling (2000 brood) fall chinook salmon from the barge. These fish were 100% adipose clipped (marked) and coded-wire tagged. We released another 3,994 fish on July 3 directly into the Snake River at LFH. These fish were refused for NPT research because of size. An additional 1,732,167 subyearlings (2000 brood) were released by the NPT in 2001; one group at Captain John, two from Big Canyon, and one from Pittsburg Landing acclimation facilities. As part of Idaho Power Company’s mitigation for fish loss associated with the construction of Hells Canyon Dam, another 115,220 subyearling (2000 brood) fall chinook were released below Hells Canyon Dam.

In 2002, all of the yearling fall chinook salmon (2000 brood) released from LFH and the acclimation sites were adipose clipped (marked), coded-wire tagged, and elastomer tagged. During April 1-11, LFH volitionally released 432,511 yearling (2000 brood) fall chinook salmon from the hatchery. The NPT released 479,360 fall chinook yearlings (2001 brood) on April 10, 2002 from acclimation facilities upstream of LGR Dam.

On June 24, 2002, LFH released 194,582 subyearling (2001 brood) fall chinook salmon from the hatchery. These fish were 100% adipose clipped and coded-wire tagged. There were two additional groups of late subyearlings released by WDFW, both of which were unmarked/untagged at release. The first group (29,059 fish) was released into the Snake River above LGR Dam at Chief Timothy Park on October 16, 2002. These fish were originally slated for NOAA research, but they were too small to PIT tag. The second group (24,573 fish) was released December 2, 2002 into the Snake River at Roosters Landing, also above LGR Dam. These were excess fish on hand at LFH after all the yearling groups were tagged. An additional 2,398,079 subyearlings (2001 brood) were released by the NPT; two groups at Captain John, two from Big Canyon, and one from Pittsburg acclimation facilities. As part of Idaho Power Company’s Hells Canyon mitigation agreement, another 171,120 subyearling (2001 brood) fall chinook were released below Hells Canyon Dam.

In 2003, from April 1-9, LFH volitionally released 518,436 yearling (2001 brood) fall chinook salmon from the hatchery. The NPT released a total of 437,633 fall chinook yearlings (2001 brood) March 30, 2003 from acclimation facilities upstream of LGR Dam.

Surveys were conducted to count fall chinook redds in the Tucannon River. In 2001 and 2002, we observed 65 and 183 redds and sampled 35 and 74 carcasses, respectively. The estimated escapement to the Tucannon River was 195 and 549 fall chinook in 2001 and 2002.

In 2001, we estimate 47.3% of the adults were LFH/Snake River hatchery origin, 35.3% were natural origin, and 17.4% were out-of-basin strays. Jacks in 2001 were composed of 60.7% LFH/Snake River hatchery origin fish, with 39.3% unassigned origin due to small sample size. In 2002, we estimate 38.0% of the adults were out-of basin strays, 31.2% were LFH/Snake River hatchery origin, 11.4% were natural origin, and 19.4% were of unknown hatchery origin. Jacks were composed of 26.7% LFH/Snake River hatchery origin fish, 23.3% out-of-basin strays, 23.3% unassigned hatchery origin fish, and 26.7% unassigned wild or hatchery origin fish.

We were unable to account for 19.2% (4,822 fish) and 6.0% (1,335 fish) of fall chinook escapement past Ice Harbor (IHR) Dam in 2001 and 2002, respectively. These estimates are calculated as the difference between the number of fish crossing IHR Dam and the numbers of fish entering LFH, spawning in the Tucannon River, and counted at LGR Dam.

Since 1990 WDFW adopted a broodstock collection protocol that allowed removal of strays from broodstock to maintain similarity to the Snake River natural origin fall chinook. In 1993 National Marine Fisheries Service (NMFS) began requiring the removal of strays at LGR Dam. The goal was to keep strays below 5% of the total run above LGR Dam. During 2001 and 2002 the stray rate above LGR was 1.9% and 1.2%, well under the level suggested by NOAA. Out-ofbasin strays were mainly (84.5%) from releases in the Umatilla River. Also included in the stray estimate were fish released from Klickitat Hatchery as well as Priest Rapids Hatchery.

The final location of wire tagged LFH/Snake River hatchery origin fish was summarized for the 2001 and 2002 return years. In 2001 yearling releases had approximately 43% of their adult detections in the Snake River, 20% in the Columbia River, and 37% in ocean fisheries. Adult detections in 2001 from subyearling releases indicated 75% were located on the Snake River, 10% were in the Columbia River, and the remaining 15% in ocean fisheries. Adults from yearlings returning in 2002 had approximately 46% of their detections in the Snake River, 15% in the Columbia River, and 39% in ocean fisheries, while subyearling returned adults were located strongly to the Snake River (67%), 9% to the Columbia River, and the balance of 24% to ocean fisheries.

We estimate that 9,361 fall chinook adults and 4,756 jacks of LFH/Snake River hatchery origin returned to the Snake River in 2001; 77% of the 18,300 which are required for mitigation. In 2002 we estimate that 11,355 fall chinook adults and 5,157 jacks of Lyons Ferry origin returned to the Snake River, 90% of the 18,300 fish required for mitigation. Jacks comprised 33.7% of the return of LFH/Snake River hatchery origin fish in 2001, compared to 9.1% wild origin jacks.

In 2002, jacks comprised 31.2% of the return of LFH/Snake River hatchery origin fish while jacks were 41.6% of the return of wild origin fish. These estimates are based on a preliminary Lower Granite Dam run reconstruction and will change when the final run reconstruction is completed.

Recommendations for the future include:

1) focus on reducing jack return rate by examining the size, time, and type of release that may be causing excess jacks;

2) pursue additional funding to build additional raceways or rearing ponds at LFH to address fish density and fish health concerns;

3) propose outlets for additional fish produced at LFH like a direct stream release of subyearlings paired with the release of subyearlings out of Captain John acclimation facility to compare survival between release strategies or encourage IDFG and Idaho Power Company to aggressively develop Oxbow Hatchery for future chinook releases;

4) summarize adult returns for LFH origin fall chinook beginning with the 1990 brood released at LFH and include in a future report;

5) complete a cooperative report with fall chinook co-managers in the Snake River basin to determine the effectiveness of programs at meeting LSRCP goals and assess the success of each release site by looking at smolt-to-adult survivals and age/sex of returns; and

6) summarize ATPase and cortisol data that has been collected over the years and include it in an upcoming report.