2006 Skagit River Wild Salmon Production Evaluation Annual Report

Skagit River Chinook returns (spring and summer/fall combined) have declined over the last fifty years. In 1999, Puget Sound Chinook salmon were listed as �"Threatened” under the Endangered Species Act (ESA). To address this poor stock status, resource managers formed the multi-agency Skagit River Chinook Work Group in 1995. A major goal of this group is to determine the factors that limit Chinook production. In addition to assessing habitat and adult returns, juvenile production monitoring was initiated, as it directly measures freshwater survival. Evaluating the biological attributes of outmigration timing and size contributes to our understanding of Chinook freshwater life history. This information is useful for flow management, habitat protection and restoration, and designing hatchery programs to minimize adverse interactions.

In 1990, WDFW initiated downstream migrant trapping in the Skagit River system in Mount Vernon. Although this project was originally directed at assessing coho smolt production (April through June), we identified and enumerated all fish captured. In 1991, through a fisheries settlement agreement with state, federal and tribal agencies, Seattle City Light (operators of several dams on the Skagit River) created the Skagit Non-Flow Plan Coordinating Committee (NCC). Beginning in 1997, this program provided funding to expand our Skagit River downstream migrant trapping project to also estimate Chinook production (January through July). This report documents our investigations for all downstream-migrant salmonids during Spring 2006, the seventeenth year that we have measured downstream migrants from the Skagit River. This year is also noteworthy as it is the last year NCC provided funding for Chinook monitoring.

As in previous seasons we used two traps â€" a floating inclined-plane screen trap (scoop trap) and a screw trap â€" to capture downstream migrants in 2006. The traps were operated from January 18 through July 31, and were fished every night and every third day unless flows and associated debris loads were excessive. The methods used to estimate Chinook abundance were changed in 2006 to improve estimate precision. In the past we used a small number of releases (four to seven groups primarily comprised of marked hatchery-produced (HOR) fish) to estimate trap efficiency. In 2006 we released 49 groups of marked natural-origin (NOR) fish to better abundance using a stratified mark-recapture approach. This technique better estimates trap efficiency under changing river conditions. These groups were marked and released above the trap. Recovery rates for these calibration groups averaged slightly higher (2.63%) than the long-term mean capture rate (2.45%) of 37 zero-age Chinook (29 HOR, 8 NORs) calibration groups that we released upstream of the mainstem traps from 1998 through 2005.

We also use mark-recapture methodology for estimating coho smolt production from the Skagit River. In 2006, as in previous years, we installed a weir trap on Mannser Creek to provide a mark group for our production estimate of coho smolts. The 2006 estimate of 735,876 NOR coho smolts was made using a pooled Peterson approach. This estimate was considerably lower than the average production from 1990 through 2005 of 1,091,590 coho smolts, and is the fourth lowest on record.

Over the season we captured 61,493 and 39,767 NOR Chinook 0+ in the scoop and screw traps, respectively. The months of January, February, March, and April accounted for 72% of the season’s catch; with about 50% of the NOR Chinook 0+ catch occurring at the mainstem traps by March 25. This migration timing is very near the average longer-term median migration date we have observed from 1997-2005 (March 27). Expanding catches for the intervals not fished estimates an additional 21,778 and 19,741 NOR Chinook 0+ would have been captured in the scoop and screw traps, respectively. Combining these projected catches with the actual catches estimates 142,779 NOR Chinook 0+ would have been caught in the two traps had we fished continuously from January 18 through July 31. Applying the newly implemented stratified mark-recapture approach to the expanded catch data yields a system production estimate of approximately 6.2-million zero-age NOR Chinook (CV = 5.85%, CI +/- 712,894). Average survival-to-migration is estimated at 11.4% based on a potential deposition of 54.6 million eggs (9,922 females and an average fecundity of 5,500 eggs/female) for the 2005 brood.

Over the previous sixteen seasons, flow during egg incubation has explained most of the inter-annual variation in our estimates of egg-to-migrant survival rates for NOR Chinook. The production in 2006 is very near the value estimated by this relationship. The high adult escapement in 2005 coupled with moderate flows during incubation and migration resulted in high catches and the favorable survival rate.

In addition to NOR Chinook, we caught a total of 16,423 ad-marked and coded-wire tagged (CWT) HOR Chinook 0+ in the mainstem traps. We estimate that, had the trap fished continuously, an additional 10,140 HORs would have been captured. The projected total catch of 26,563 HOR Chinook includes 9,103 summers (released at Countyline Ponds), 7,917 falls (released at Baker River) and 9,542 springs (released at Marblemount Hatchery). Application of the stratified mark recapture efficiency data from NOR fish to expanded catches yields a combined estimate of just over 1.1 million HOR Chinook 0+. Relating this estimate to the 677,882 HOR Chinook released shows we overestimated hatchery production. We believe this high production estimate and the high recapture rates of HOR Chinook, combined with fairly high flows at release times, indicate good survival of the 2005 brood hatchery groups from release to the trap site.