Annual Report 2011Project No. 1982-013-03Annual Stock Assessment - CWT (USFWS)ByStephen M. PastorU.S. Fish and Wildlife ServiceColumbia River Fisheries Program Office1211 SE Cardinal Court, Suite 100Vancouver, WA 98683February 2013Funded ByBonneville Power Administration

INTRODUCTIONIn 1989 the Bonneville Power Administration (BPA) began funding the evaluation of productiongroups of juvenile anadromous fish not being coded-wire tagged for other programs. These groupswere the "Missing Production Groups". Production fish released by the U.S. Fish and WildlifeService (FWS) without representative coded-wire tags during the 1980s are indicated as blankspaces on the survival graphs in this report. This program is now referred to as "Annual StockAssessment - CWT"The objectives of the "Annual Stock Assessment" program are to:-estimate the total survival of each production group,-estimate the contribution of each production group to fisheries, and-prepare an annual report for USFWS hatcheries in the Columbia River basin.Coded-wire tag recovery information will be used to evaluate the relative success of individualhatchery brood stocks. This information can also be used by salmon harvest managers to developplans to allow the harvest of excess hatchery fish while protecting threatened, endangered, orother stocks of concern.All fish release information, including marked/unmarked ratios, is reported to the Pacific StatesMarine Fisheries Commission (PSMFC). Fish recovered in the various fisheries or at the hatcheriesare sampled to recover coded-wire tags. This recovery information is also reported to PSMFC.This report has been prepared annually starting with the report labeled “Annual Report 1994”.Although the current report has the title “Annual Report 2010”, it was written in fall of 2012through early winter 2013 using data available from RMIS at that time; and submitted as final inMarch 2013. The main objective of the report is to evaluate survival of groups of hatchery fishwhich have been tagged under this ongoing project.

METHODSThe Annual Stock Assessment Report reports coded-wire tagging for the most recently completedcontract period, and evaluates the survival and contribution of fish tagged, raised and releasedat National Fish Hatcheries in the Columbia River Basin.Release information used in this report is collected with the U.S. Fish and Wildlife ServiceColumbia River (information) System (CRiS). Information prior to the Columbia River Basin wideimplementation of CRiS, and from USFWS hatcheries in Idaho, is obtained from the interagencyRegional Mark Information System.Lists of coded-wire tags are obtained from the CRiS sr80s file by use of the CWTetc program.This currently involves the additional step of downloading Dworshak and Kooskia releaseinformation from the RMIS database, and adding it to the sr80s file. In past years numerousdiscrepancies have been noted between the original reports of releases, and those in RMIS.Recovery information is obtained from the PSMFC Regional Mark Information System (RMIS) codedwire tag database web site. This database is continuously being updated by the contributingagencies: California Fish and Game (CDFG), Canadian Department of Fisheries and Oceans (CDFO),Oregon Department of Fisheries and Wildlife (ODFW), Washington Department of Fisheries andWildlife (WDFW), and US Fish and Wildlife Service (FWS); and the updates are reflected annuallyin this report.Coded-wire tag recovery information is retrieved in the TS1 (Tag Summary) format. The TS1 reportcontains both the observed number of recoveries, and the estimated number of recoveries based onthe sampling rate. The TS1 report is used precisely because it is a Summary. The number ofindividual recoveries, and the number of individual recovery sites preclude there use in thisreport. The TS1 report summarizes individual recoveries and recovery sites into broad categoriesbased on combinations of geographic and other criteria, and provide a consistent means ofreporting from year to year.It should also be noted that fisheries in some tributaries such as the Clackamas River, and itstributary Eagle Creek, are poorly sampled (or not at all) for recovery of coded-wire tags. Stateagencies often rely on harvest estimates based on sport license returns in these tributaries, andthis information is not available through RMIS and the TS1 format.TS1 reports were downloaded from RMIS in fall of 2012. These TS1 reports are downloaded in ASCIIformat. A dBASE V program transforms these ASCII files into a single dbf file.A Stock Assessment Reference Document is prepared for each hatchery, brood year, and species.Because many fish were released without representative coded-wire tags before the Annual StockAssessment program began, a single Production Expansion Factor (PEF - the total number of fishreleased divided by the total number of tagged fish released) is calculated for each hatchery,brood year, species, and stage of fish released. This PEF is used to expand estimated recoveryinformation for untagged fish released along with tagged fish, and to determine the overallcontribution and survival rate for each facility.Until the late 1990s, the adipose fin was removed from all fish receiving a coded-wire tag. Themissing adipose fin facilitated the recovery of tags from returning or harvested jacks andadults.In the late 1990s the goal of protecting weak, threatened, or endangered populations of fish,while maintaining fisheries on healthy populations, led to the removal of the adipose fin frommost hatchery fish. The "mass marking" of hatchery steelhead, Coho, and Chinook makes it possibleto harvest only hatchery fish. Wild fish with adipose fins are not harvested in “selectivefisheries". In order to assess the success of selective fisheries, and to serve as an “index” forwild fish populations, some hatchery fish are coded-wire tagged, but not adipose fin clipped.These fish will not be harvested in any selective fisheries that may occur. A dbase program waswritten to expand recoveries for each coded-wire tag, rather than calculating a ProductionExpansion Factor. This program is used for all current brood years, and has now been used formany older brood years beginning with brood year 1990.Stock Assessment Reference Summary printouts list the following information for each brood year,species, hatchery, and stage released at the hatchery: release information, the total number ofobserved recoveries, where recoveries occurred, the number of expanded recoveries from the PSMFCTS1 report, the number of recoveries expanded to include unmarked fish released, and a summary ofwhere fish were recovered. The most recent brood years have been reprocessed, and all brood yearsfor all hatcheries and species are included in this report. Text describing the major attributesof the contribution for each hatchery, species, and brood year is prepared and included in thereport. Graphs of survival and relative proportion of recoveries in major areas are prepared andincluded in the report.

In November 2008 the program that summarizes data for the Fisheries graphs was amended to addharvest in the Estuary Sport fishery to the Columbia R. Sport numbers."Residualized" fish, or "mini-jacks" from yearling releases, are not included in estimates ofsurvival.In 2009 the SA program was refined to perform the second expansion, which “corrects” for the factthat not all released fish are coded-wire tagged, and expands total recovery for the untaggedand/or unmarked fish for each coded-wire tag, recovery site, and year. The effect of this changewas noticeable even at the Warm Springs NFH facility, where 100% of released fish are coded-wiretagged before being released.The SAsumRY.prg creates a file imported into the Releases and Returns tables that follow thegraphs of survival rates, and fisheries for each hatchery and species.RESULTSFour hundred and seven "Annual Stock Assessment" tags were recovered at National Fish Hatcheriesin 2012, while the number of fish tagged under this program was 175,751.A brief description of the estimated survival and contribution for each species raised andreleased at national fish hatcheries follows. These descriptions are followed by graphs for eachhatchery and species.

Abernathy Fish Technology CenterAbernathy Fish Technology Center (FTC) is located 14 miles west of Longview, Washington, onAbernathy Creek, approximately three miles upstream from its confluence with the Columbia Riverat an altitude of 175 feet above sea level. Abernathy FTC began operations in 1959. From 1980through the 1990s, lower river tule fall Chinook were the only species reared on a productionbasis at Abernathy as part of Mitchell Act (NOAA Fisheries) funding. Information of these tulescan be found at the end of this report.Columbia River Program Fisheries Office marking crews have been coded-wire tagging steelhead atAbernathy since January 2003. CRFPO personnel have also read wire from recovered adults. The RMISdatabase contains one recovery from these tagged fish.

Carson National Fish HatcheryCarson National Fish Hatchery (NFH) is located 13 miles northwest of Carson, Washington, at theconfluence of the Wind River and Tyee Springs (River Mile 18), at 1,180 feet above sea level.Carson NFH began operation in 1938 by rearing and releasing fall Chinook salmon and trout.In 1956, the hatchery was remodeled under the Mitchell Act. Construction of a fish ladder atShipperd Falls (River Mile 2.1) in 1955 made it possible for spring Chinook to pass upstream tothe hatchery. Trapping of spring Chinook at Bonneville Dam began in 1955, after Washington shoretrapping facilities were completed, and continued through 1961. Those trapped fish were used toestablish the Carson run of spring Chinook in the Wind River. Other species such as steelhead,brook trout, rainbow trout, kokanee, and coho have also been raised at Carson. Coho were raisedas late as 1981. Current production involves adult collection, egg incubation and rearing ofspring Chinook salmon.Please note that sport and tribal harvest based on recovery of coded wire tags in the ColumbiaRiver as well as the tributaries (for example Wind River) are all reported as Columbia Riverharvest.Brood year 1982 to 1985 spring Chinook from Carson were marked with coded-wire tags for a densitystudy. The average total survival of these brood years is 0.22%. The majority of off stationrecoveries were in the freshwater sport fishery. There were an estimated 20 recoveries of broodyear 1982 and 1983 fish in Canadian waters. An estimated 43 recoveries of brood year 1985 fishoccurred in ocean fisheries in Alaska, Canada, and Washington.Because of a WDFW fish marking study at Carson, WDFW sampled returning adults and originallyreported recoveries for return years 1993 through 1996. During the change over from format 3.2 to4.0, USFWS reported these recoveries.The survival rate for Carson brood year 1988 is 0.4044% using the rd2 program which expands eachcoded-wire tag, rather than using a PEF, and including one additional expanded freshwater sportrecovery reported by WDFW. The majority of contribution to fisheries was in the Columbia Riverfreshwater sport, expanded to 5,339. Recoveries in the treaty ceremonial fisheries were expandedto a catch of 1,023.Brood year 1989 was also part of the fish marking study conducted by WDFW. The estimated survivalfor this brood year is 0.1368%, less than a third of the previous brood year. The majority offish taken off station (2,095) were taken in the freshwater sport fishery reported by WDFW. Twoobserved recoveries in the Washington ocean troll fishery were expanded to a total of 12 fishcaught.The survival rate for brood year 1990 is 0.0778%, a total of 1,801 fish from a release of over 2million. A third of the fish entering the Columbia River were harvested before reaching Carson.Most of these recoveries, estimated at 125, were freshwater sport reported by WDFW. Treatyceremonial fishery recoveries reported by ODFW show 32 fish taken, followed by 27 in the ColumbiaRiver sport fishery.Brood year 1991 survival is now estimated to be 0.0239%. This is less than brood year 1990 andthe lowest to date. The largest off station take of fish was the ODFW reported treaty ceremonialharvest of 69 fish. Four fish were recovered in WDFW spawning ground surveys, expanded to 12.This was the last brood year for the WFDW mark study.Survival for brood year 1992 is 0.6145%, the highest since brood year 1988. An estimated 82 fishwere harvested in the California ocean troll fishery, an unusual event. Since all of the codedwire tags released with brood year 1992 were used for a density study, none of the tag codesrepresents the majority of fish released. Recoveries for this brood year at Carson NFH wereoriginally reported by WDFW.The 1993 brood year now has the fifth highest survival for this hatchery at 0.4371%. An estimated42 fish were harvested in the California ocean troll fishery as jacks. The harvest of these fishoff of California occurred the same year as the harvest of 82 fish from brood year 1992. WDFWfreshwater sport fishery recoveries are expanded to a harvest of 4,494 fish, nearly as many asreturned to the hatchery. Since all of the coded-wire tags released with brood year 1993 wereused for a new density study, none of the tag codes represents the majority of the fish released.Brood year 1994 survival is now estimated at 0.1243%. There are an expanded 882 fresh water sportrecoveries, 1,082 expanded returns to hatcheries, and 165 expanded spawning ground recoveries.This equals a total of 2,141 expanded recoveries for the 1994 brood year.There are an additional 4 PSC expanded WDFW freshwater sport recoveries this year, increasing theestimated survival for brood year 1995 to 0.3770%, in the upper third of successful brood years

for Carson NFH. There have been an estimated 997 expanded off station recoveries from these fish,all in the Columb