UMPQUA RIVER FALL CHINOOK SALMON ESCAPEMENT INDICATOR STOCK PROJECT

Transcription

1 UMPQUA RIVER FALL CHINOOK SALMON ESCAPEMENT INDICATOR STOCK PROJECT CUMULATIVE PROGRESS REPORT for work conducted pursuant to Natonal Oceanc and Atmospherc Admnstraton Award Numbers: : NA87FP : NA97FL : NA07FP : NA17FP : NA17FP2458 and U.S. Secton, Chnook Techncal Commttee Project Numbers: N98-17, N98-16, N99-07, N99-09, C00-12, N00-04, N01-18 and C02-06 Sam Moyers Jody Whte Bran Rggers Mar Wllams Chrs Sheely Hal Weeks Coastal Chnook Research and Montorng Project Oregon Department of Fsh and Wldlfe Marne Resources Program Roseburg & Newport, OR June 2003 Umpqua Cumulatve Progress Report doc

2 TABLE OF CONTENTS FIGURES AND TABLES...3 INTRODUCTION...4 STUDY AREA...7 DATA COLLECTION METHODS...8 Mark-Recapture...8 Carcass Recovery...9 Age Composton...10 Rado Telemetry...10 Creel Survey...10 DATA ANALYSIS...11 Spawner Escapement...11 Age and Sex Composton...14 Rado Telemetry...15 Creel Survey...16 RESULTS...18 Spawner Escapement...18 Age and Sex Composton...25 Spawnng Survey Calbraton...31 Rado Telemetry...31 In-Rver Harvest...32 DISCUSSION...33 ACKNOWLEDGEMENTS...35 REFERENCES...36 APPENDIX A...37 APPENDIX B...39 Umpqua Cumulatve Progress Report doc

3 Lst of Fgures Fg 1 Umpqua Rver System Fg 2 Tmng of Taggng Fg 3 Predcted vs Actual Spawner Escapements n the South Umpqua Rver Lst of Tables Table 1 Annual counts of fall chnook passng Wnchester Dam, North Umpqua Rver Table 2 Redds counted n South Umpqua basn aeral fall chnook spawnng surveys Table 3. Summary table of fall chnook escapement estmates wth confdence ntervals, bas and precson estmates. Table 4 Stratfed, fully pooled and Darroch escapement estmates Table 5 Sex and Age Composton of fall chnook n the South Umpqua Table 6 Aeral redd count calbraton aganst spawner escapement estmates Table 7 Dstrbuton of rado tagged fall chnook n the Umpqua Rver system n 2001 and Table 8. Estmates of recreatonal harvest of Umpqua fall chnook based on angler-returned catch cards. Umpqua Cumulatve Progress Report doc

4 EXECUTIVE SUMMARY Ths Umpqua fall chnook escapement ndcator project has been underway snce 1998, wth a focus on the South Umpqua/Cow Creek porton of the system where the majorty of fall chnook are understood to spawn. Fall chnook spawner abundance estmates by year as developed through mark-recpature methods are: Spawner Abundance Estmate 95% Relatve Precson Year , % , % , % , % , % In 2001, we started taggng n the manstem Umpqua wth the objectve of developng a full basn estmate of fall chnook. The estmates developed (6,600 n 2001 and 13,000 n 2002) suggest that 80% of the Umpqua fall chnook go nto the South Umpqua/Cow Creek subsystem. We rado tagged 31 fall chnook n 2001 and 72 fall chnook n Trackng these fsh shows that many ascend nto the South Umpqua/Cow Creek subsystem, but that a substantal proporton of spawnng chnook use the lower South Umpqua and the manstem Umpqua. Ths suggests that the spawnng populaton may be much larger than the table presents. Spawnng surveys n the South Umpqua are conducted by aeral counts of chnook salmon redds. We have three years of data to calbrate redd counts aganst spawnng escapement numbers (1999 to 2001, no flghts were conducted n 2002 due to fundng constrants) and we see an average of 3.2 chnook salmon per redd wth a farly close coeffcent of varaton of 17%. As n the other basns, ths populaton (excludng jacks) s domnated by age 3 and 4 ndvduals. Recreatonal harvest of fall chnook n the Umpqua has averaged 1695 fsh from 1998 through 2001 as estmated by Oregon punch cards. Creel survey estmates of harvest are 1436 (76.5% of the punch card estmate) n 2001, and 948 n 2002 (no punch card estmate avalable). INTRODUCTION The Oregon Department of Fsh and Wldlfe (ODFW) s conductng a mult-year, mult-basn research study to develop methods that provde relable estmates of fall chnook salmon (Oncorhynchus tshawytscha) spawner escapements n Oregon coastal rvers. Fall chnook salmon orgnatng n Oregon coastal rvers north of Elk Rver are north-mgratng and vulnerable to fsheres off of southeast Alaska and Brtsh Columba. The U.S. Canada Pacfc Salmon Treaty establshed the Pacfc Salmon Commsson (PSC) to provde a framework to manage salmon fsheres. The 1999 modfcaton to the Treaty defnes an aggregate abundance based management (AABM) regme whereby harvests wll vary wth abundance. A broader goal of ths treaty s to restore and rebuld producton of naturally spawnng chnook (PSC 1997). Umpqua Cumulatve Progress Report doc

5 In order to accomplsh these goals and montor the rebuldng of specfc chnook stocks, the PSC s Chnook Techncal Commttee (CTC) assesses three elements for each stock: 1) spawner escapement levels, 2) fshery harvest and explotaton rate, and 3) subsequent producton from spawners. Data on geographcally dverse chnook stocks provded by PSC partcpants (Canada and U.S. state, federal and trbal agences) are ncorporated nto the PSC s Chnook Model that generates yearly pre- and post-season cohort abundance estmates. These estmates are used by the PSC to montor the relatve health of chnook stocks under PST jursdcton and to set ocean harvest levels. Currently, Oregon coastal chnook stock assessment nformaton comes from a standard spawner survey program, a voluntary angler-returned catch card system, and two explotaton rate ndcator stocks. These tradtonal montorng programs do not supply the CTC wth adequate nformaton that s requred for the management and rebuldng of Oregon s coastal chnook stocks. ODFW has conducted surveys of standard spawnng ground reaches for over ffty years to montor the status of chnook stocks along coastal Oregon (Jacobs et al. 2000). Coast-wde, a total of ffty-sx standard ndex spawner surveys (45.8 mles) are montored throughout 1,500 stream mles on an annual bass to estmate peak escapement levels and track trends of north-mgratng stocks. Although counts n these standard surveys may adequately ndex long-term trends of spawner abundance, they are not adequate for dervng acceptable annual estmates of spawner escapement. The Umpqua Rver s a sgnfcant contrbutor of north mgratng fall chnook on the md-oregon coast. Umpqua Rver fall chnook have had lttle nfluence from hatchery-produced fsh, thus makng ths stock a logcal canddate to become an escapement ndcator stock for the md-oregon coast (MOC) stock aggregate. A bologcally based escapement goal would need to be developed for t to be adopted as an escapement ndcator stock. The Umpqua Rver s composed of three major trbutares: South Umpqua, North Umpqua, and Smth Rver. Most fall chnook spawnng takes place n the manstem Umpqua, the South Umpqua and Cow Creek, a major trbutary of the South Umpqua (Fg 1). The chnook run s montored through counts at Wnchester Dam on the North Umpqua near Roseburg (generally < 200 fsh annually) (Table 1); and aeral counts of redds on the South Umpqua and Cow Creek (Table 2). Index chnook spawnng surveys have been conducted on trbutares below Smth Rver trap and Mll Creek sporadcally for the last 5 years. (ODFW unpublshed data). Table 1. Year Fall Chnook Counts at Wnchester Dam, North Umpqua Rver Count Umpqua Cumulatve Progress Report doc

6 Table 2 Adult Spawner Populaton - Redd Comparson for South Umpqua Basn, Oregon Redd Counts (flght) Cow Year Estmated Total S. Umpqua Creek Redd Counts (float) Populaton manstem Fsh/Redd Fsh/Redd notes ,477 1, note NA NA NA Notes: 1. Douglas County OR cut fundng for survey flghts n Adult spawner estmate s very prelmnary adult spawner estmates based on mark-recapture methods. Pre 1998 adult spawner estmates are based on 3.34 fsh/redd tmes number of redds 4. Float redd counts n 2002 were ncomplete Umpqua Cumulatve Progress Report doc

7 STUDY AREA The Umpqua Rver dranage orgnates at the Cascade mountan crest, and covers about 14,245 km 2, most of whch s accessble to anadromous fsh (Fgure 1). Prncpal trbutares are the Smth, North Umpqua, and South Umpqua rvers. The South Umpqua and Cow Creek (a major trbutary), account for the majorty of the fall chnook spawnng area wthn the Umpqua basn. Only the lower 65 mles of the South Umpqua s used by fall chnook, and the majorty of spawnng occurs between Rver Mle 18 and Rver Mle 47.5 at Cow Creek. In Cow Creek the majorty of spawnng occurs n the lower 26 mles of stream. Fgure 1. Umpqua Rver dranage wth capture stes noted. OBJECTIVES The goal of the Umpqua Escapement Indcator Project s to precsely estmate the annual escapement at age of adult chnook salmon to the Umpqua Rver, and to annually update a brood-year reconstructon for that stock. These data wll be the bass for a stock-recrutment analyss necessary to estmate a bologcally-based spawner escapement goal. These data wll also permt post-season assessment of management success n meetng escapement goals, and wll enable the managers to calbrate escapement estmates to less precse survey methods. Specfc objectves of ths project to meet the goal are: Umpqua Cumulatve Progress Report doc

8 1) Estmate the total escapement of adult chnook from ocean fsheres nto the Umpqua Rver wthn ± 25% of the true value 95% of the tme and to estmate the age specfc proportons of the escapement wthn ± 5% of the true value 95% of the tme. Specfc tasks that must be completed to acheve the overall objectve are: a) Estmate the sport harvest of chnook salmon n Umpqua Rver such that the estmate s wthn ± 25% of the true value 95% of the tme, and estmate age/sex specfc proportons of that harvest such that the estmate s wthn ± 5% of the true value 95% of the tme (2001 and 2002 only). b) Estmate the spawnng abundance of fall chnook salmon n the South Umpqua Rver and Cow Creek such that the estmate s wthn ± 25% of the true value 95% of the tme, and estmate age and sex specfc proportons of the spawnng abundance such that estmates are wthn ± 5% of the true value 95% of the tme. Begnnng n 2000, addtonal markng n the manstem Umpqua Rver enables a basn-wde spawner abundance estmate n addton to the S. Umpqua/Cow Creek estmate. 2) Estmate the dstrbuton of spawnng adult chnook salmon between manstem and trbutary habtat strata based on rado telemetry. 3) Derve an expanson factor that relates the mark-recapture populaton estmate to aeral redd counts. DATA COLLECTION METHODS Mark-Recapture Lower Manstem We estmated spawnng escapement of adult ( > 600 mm fork length) fall chnook escapement wth a two-event stratfed Peterson mark-recapture experment. Intally, work began at the Happy Valley wer (South Umpqua rver mle 18) where returnng fall chnook were marked and released to estmate spawner abundance n the South Umpqua/Cow Creek porton of the system. Ths became a dual two-event experment wth the addton of efforts to develop a basn-wde estmate begnnng n Fall chnook were captured usng tangle nets at three stes on the lower manstem Umpqua (RM 23, 29.5, 40). (Fg 1). These three stes are located n freshwater areas of the manstem to avod handlng durng the freshwater to saltwater transton phase. The ste at RM 29.5, known as Famly Camp, s the prmary ste. The stes at RM 23 and 40 were explored and used durng 2001; lower manstem tangle nettng was done exclusvely at Famly Camp n These stes are located below all manstem-spawnng areas wth the excepton of Mll Creek, Dean Creek, Scholfeld Creek, and Smth Rver. We captured and marked returnng adult fall chnook wth tangle nets at these rver stes from md-august and to md- October. Nettng occurred at nght to reduce net avodance and angler conflcts. Four person taggng crews captured chnook durng ten to twelve hour work sessons. Daly logs were kept to record each net set, water temperature, tdal flow when pertnent, number of fsh captured, and mortaltes. Duraton of taggng effort n the lower manstem Umpqua s constraned by encounters wth coho salmon that are lsted as threatened under the Endangered Speces Act. The Department s permt condtons for ths project requre us to mnmze our take of coho salmon, and hence we end nettng and markng operatons n manstem Umpqua before the full run of fall chnook salmon has passed by the tangle net ste. Umpqua Cumulatve Progress Report doc

9 The capture crew mantaned tactle or vsual contact wth the net at all tmes to ensure fsh would be observed and removed quckly. Fsh were generally removed from the net less than a mnute after ts presence was detected. Captured fsh were held n an aerated lvewell contanng artfcal slme to mnmze stress and bacteral nfecton due to handlng. All captured chnook salmon were placed nto a hooded cradle for taggng and nspecton. They were sampled for length (fork length), sex, and scales (age composton), and marked. A sngle sequentally numbered colored (yellow) anchor tag was placed on the left sde of the dorsal fn. Yellow anchor tags were used to ncrease vsblty of marked fsh n the fsh countng tapes at Wnchester Dam. A left operculum punch, usng a _ paper punch, was admnstered as the secondary mark. Begnnng n 2002, we dscontnued the use of numbered anchor tags. Rather, fsh were marked wth operculum punches and clppng the left axllary appendage. Locaton and number (one or two) of punches served to dentfy the week of capture and markng. After taggng each fsh was allowed to recover n the aerated lve well and subsequently released to contnue ts upstream mgraton. When several fsh became entangled n the net, feld crews were responsble for ensurng that no fsh were left n the net to suffocate. If the feld crew could not recover fsh from the net n a tmely manner, the amount of net beng fshed was reduced. Chnook that appeared hghly stressed were placed n the recovery lvewell and released wthout samplng. Happy Valley Trap, South Umpqua Manstem Fall chnook salmon were also captured and marked at a floatng wer ste at rver mle 18 on the South Umpqua (Fgure 1). The wer, consstng of 19 four foot wde by twenty foot long panels, forced adult chnook nto a trap. The trap was fshed twenty-four hours a day from late-september to the frst week of November. Chnook salmon were removed from the trap and placed nto a hooded cradle for taggng, measurements, and nspecton. Fsh were frst checked for marks from the lower manstem taggng. If a mark was found, tag numbers, color, operculum marks, condton of each fsh were recorded, and then gven an addtonal left operculum punch. Unmarked fsh were sexed, measured (fork length), scales taken for age analyss, and marked wth a sequentally numbered gray Floy anchor tag and a left operculum punch. Multple marks were used to mnmze tag loss as well as ensure accurate dentfcaton of carcasses on the spawnng groups. In 2002, we dscontnued the use of numbered anchor tags as dentfcaton of ndvdual fsh was no longer deemed mportant. Rather, fsh were marked wth a rght operculum punch. Operculum punches were coded by locaton and number to ndcate the week of markng. Carcass Recovery on Spawnng Grounds The second part of the two event mark-recapture experment nvolves actvely locatng chnook carcasses throughout the rver basn; most of these were upstream of Happy Valley Trap. The South Umpqua and Cow Creek were dvded nto multple floatng spawnng surveys (float). Cow Creek spawnng surveys conssted of four floats that total 27 mles of stream. South Umpqua surveys were comprsed of sx floats above Happy Valley trap (58 stream mles) and two floats below the trap (18 stream mles). Each survey segment was from 8 to 12 mles and ncorporated multple EPA reaches (from four to eght per segment). Each float was surveyed by two catarafts to ncrease survey effort and for safety. Locatons of known, hgh-densty areas of fsh carcasses were emphaszed durng survey perods. Only carcasses wth ntact opercula were used for the second capture event. Carcasses sampled were examned for tags, fn clps and sex, measured for fork length and had scales taken for age analyss. Spawnng Survey Calbraton The survey tme seres montorng fall chnook spawner n the South Umpqua system has been by aeral counts of redds made at two tmes durng the spawnng season. Generally, flghts are made once n late October and once n the thrd week of November. Durng each flght, chnook redds are dentfed and counted. An annual ndex s derved from the peak number of redds between the two flghts (Table 2). Ths seres of survey flghts has been fnanced by Douglas Umpqua Cumulatve Progress Report doc

10 County, OR. Due to sharp county fundng reductons, no aeral counts of redds were made durng 2002, but we expect that they wll be resumed n Age Composton Samplng Scales were collected from all chnook tagged and from all unmarked carcasses examned for tag recovery. Four to fve scales were taken from each fsh. Scale samples were placed nto small paper envelopes untl they could be mounted on gummed cards n the laboratory. An acetate mpresson of each scale was produced usng a heat press. Experenced staff determned age by vsual nterpretaton. Two separate readers ndependently aged each sample and dsagreements were resolved by a thrd jont readng. Fsh age was determned by countng wnter annul. Total age was computed as the count of all annul plus one. All bologcal data was recorded drectly onto the scale envelope. Due to tme lmtatons and the volume of scales collected across ODFW research projects, readers took systematc samples that are representatve of the run. Rado Telemetry Rado telemetry was used n 2001 and 2002 to provde nformaton about the dstrbuton of fall chnook spawners n manstem and trbutary habtat areas. Ths nformaton s needed to further calbrate the aeral counts of redds wth the projects s spawner abundance estmates. Fall chnook were rado-tagged n the lower manstem Umpqua durng the capture and markng porton of the project. One out of every four captured and marked chnook receved an orally nserted, esophageal rado-transmtter. Transmtters operated from Mhz to MHz, and transmtted a unque sgnal allowng dentfcaton of ndvdual fsh. Transmtters have an expected battery lfe of one year and two szes were used durng the project. A 3- V transmtter weghng 21.9g was used for small adult chnook, whle a 7-V transmtter weghng 39.2g was used on medum and large adults. Transmtter weght dd not exceed 2% of body weght for tagged fsh. Tagged chnook were montored two to three days per week throughout mgraton and spawnng. ODFW bologsts drove the study area several tmes per week wth a portable recever, scannng the frequences of tagged chnook. Physcal locaton, sgnal strength, weather and flow condtons, and pertnent comments were recorded for all detectons. Vsual observatons of tagged chnook were attempted when possble. Weekly arcraft trackng n collaboraton wth the Oregon State Polce was also employed. Two fxed telemetry statons were employed n 2001, but dd not perform adequately; these are not ncluded n our analyses. Data was entered nto an Access database for analyss by ODFW bologsts. Two rado tags were returned by angles n each of 2001 and Creel surveyors encouraged anglers to report any captured and released rado-tagged chnook that occurred durng the 2001 and 2002 Umpqua Rver recreatonal salmon fshery. Creel Survey Recreatonal chnook salmon harvest n the Umpqua Rver was estmated from data collected by a stratfed random creel survey conducted throughout the fshng season (July through November) n 2001 and Rovng surveys were used to make angler or boat counts, to determne effort (pressure counts) and to conduct angler ntervews throughout the fshery. Dependng on the angler type, a rovng-access survey or a rovng-rovng survey desgn was Umpqua Cumulatve Progress Report doc

11 employed (Pollock et al. 1994). Rovng-access surveys were used n stuatons where anglers concentrated at known locatons (e.g. boat launches), and could be ntervewed upon completon of fshng. Rovng-rovng style surveys were used n stuatons where anglers were wdely dstrbuted (e. g. bank anglers), and the surveyor moved throughout the fshery ntervewng anglers whle they were stll fshng. Boat and bank anglers were surveyed on the manstem Umpqua; chnook harvest s not allowed on the South Umpqua Rver. Surveys were conducted from August through November. The creel survey was stratfed by catch area, month, day (weekend, weekday), and angler type. Anglers were separated nto three groups: shore anglers, prvate boat anglers, and guded anglers. Intervews collected nformaton on the number of hours fshed, number of anglers n the boat or on shore, the number of salmonds by speces caught or released, target speces, and whether bat or lures were used. Data was entered onto paper forms or hand-held electronc dataloggers. Fsh were sampled for scales, length (FL), sex, and the number and types of fn marks. If an adpose fn was mssng, the snout was removed for future tag decodng. Anglng counts were conducted by drvng the rver n each catch area at three equally spaced ntervals, and countng all people fshng. Counts took thrty mnutes and were consdered nstantaneous. Upon completon of counts, surveyors conducted angler ntervews untl the next scheduled count. Non-anglers n the catch area were also ntervewed n order to estmate use by non-anglers n and to approprately adjust the effort count. Surveyors also sampled boats at boat launches when the anglers fshng trp was complete. Future Genetc Analyses The number of dstnct chnook races or breedng groups n the South Umpqua Rver s not known. A small run of sprng chnook exsts n upper South Umpqua. Based on run tmng and spawnng observed n the South Umpqua that there may be more than one dstnct breedng populaton of fall chnook. ODFW feld crews collected a rayed fn clp from chnook collected by the brood program. Brood fsh were collected throughout the chnook run and should provde a representatve sample of run tmng. Collected tssue samples were stored n ethanol and are archved wth Dr. Mchael Banks of OSU s Hatfeld Marne Scence Center. Dr. Banks wll be collaboratng wth other coastal labs n the establshment of a DNA baselne for fall chnook that wll be a sgnfcant frst step toward genetc stock dentfcaton. DATA ANALYSIS Spawner Escapement Estmates The Chapman verson of the Peterson mark/recapture formula was used to estmate fall chnook escapement above trap and nettng stes: where ( M + 1)( C + 1) ( R + 1) Nˆ = -1 Nˆ = the estmated populaton of fall chnook above the markng ste for calbraton ste. M = the number of fall chnook marked C = the number of fall chnook recovered on the spawnng grounds. R = the number of recovered tagged fall chnook. The usual assumptons for use of the pooled Peterson estmator are: Umpqua Cumulatve Progress Report doc

12 1) a. all fsh have an equal probablty of beng marked at the trap ste; or, b. all fsh have an equal probablty of beng nspected for marks; or, c. marked fsh mx completely wth unmarked fsh n the populaton between events; and, 2) there s no recrutment to the populaton between capture events; and, 3) there s no trap nduced behavor ncludng mortalty; and, 4) fsh do not lose ther marks and all marks are recognzable. We subjectvely evaluated each assumpton to assess the potental valdty of usng the pooled Peterson model. Equal probablty of capture n the frst or second event (Assumpton 1a and 1b) probably dd not occur; there s an understood bas aganst fndng smaller carcasses n spawnng ground surveys. Assumpton 1c, equal mxng of unmarked and marked fsh, was crtcal n usng the pooled model for estmatng chnook abundance. To estmate f there was random geographc (rver sub-basns or trbutares) and temporal (weekly) mxng of marks, the ratos of marked to unmarked fsh were compared between strata usng ch-square analyss. If a sgnfcant dfference was observed, a stratfed model was used (Darroch 1961; descrbed below). The estmate generated by the stratfed model was then compared to the pooled model estmate, f they dd not dffer by more then 10% the pooled model was used. By usng the stratfed model or reduced models (ndvdual estmates for several sze categores), the estmate should be less based than wth the pooled model but precson s worse. Therefore, f the dfference, or bas, between the pooled model and the alternatve model s small, then the pooled model wth the better precson estmate should be used. Sze selectvty n the frst and second capture events (Appendx A) was addressed by preparng sze-stratfed abundance estmates as a precauton aganst dfferng tag recovery rates for each sze. If the sze stratfed abundance estmate dd not dffer from the pooled estmate by more than 10%, then the pooled estmate was used to mprove precson. In order to use carcasses for sze analyss, MEPS length was converted to fork length usng smple lnear regresson based on recaptured fsh for whch we had both MEPSand fork lengths. Assumpton 2 does not apply to ths stuaton. Only adult chnook salmon mgratng upstream of the capture ste were used n the mark-recapture study and recrutment to the populaton s not possble. Assumpton 3 was avoded n the second capture event by usng actve samplng technques and utlzng multple capture technques to collect tags wthn the spawnng areas. However, for the frst event, trap nduced behavor could occur and ths was estmated as dscussed above for age/sex selectvty. Mortalty due to handlng could be a problem wth taggng studes, however, usng anecdotal nformaton from recovery of carcasses near the taggng stes, there was mnmal pre-spawn mortalty observed. Tag loss (assumpton 4) s assumed zero wth the applcaton of mutlaton marks. Feasblty studes conducted n 1998 and 1999 n the South Fork Coos Rver and North Fork Nehalem Rver ndcated operculum punches were, where the use of an anchor tag and a operculum punch were employed, found no nstances where an anchor tag was dentfed wthout an assocated operculum punch. From feld data, when projects used anchor tags, operculum punches and axllary clps, at least one of the multple marks was observed f a fsh was tagged. We therefore assumed all mutlaton marks wll be seen on fsh f present and that at least one of the marks wll be observed by traned feld crews f a fsh was marked n the frst capture event. Carcasses recovered on spawnng grounds wthout tags and wth mssng opercula could not be assgned to marked or unmarked categores; therefore these fsh were excluded from abundance calculatons. Umpqua Cumulatve Progress Report doc

13 As mentoned above, a stratfed estmator was used f ether of the two followng condtons were not met: 1) the recovery probabltes are smlar between all strata; or, 2) the tagged to untagged ratos are constant between recovery strata. Analyss methods for the stratfed estmate followed the descrptons n Arnason et al. (1996) and Schwarz and Taylor (1998) and used the program SPAS (Stratfed Populaton Analyss System). When usng the stratfed estmator the normal pooled model assumptons are expanded to nclude: 1) all fsh have a non-zero probablty of beng found n the recovery strata and all fsh n the recovery strata were present n one of the ntal capture strata; and, 2) all tagged and untagged fsh n each recovery stratum have equal probablty of beng sampled; and 3) all tagged fsh released n each capture area have the same probablty of movement to the recovery strata as well as the tagged and untagged fsh move wth the same probablty dstrbuton. For the pooled model estmator, we estmated varance, bas and confdence ntervals of the populaton estmate wth a bootstrap method (Buckland and Garthwate 1991, Mooney and Duval 1993). The fate of chnook that pass by each trappng faclty were dvded nto several capture hstores to form an emprcal probablty dstrbuton (EPD) as follows: 1) marked and recaptured on the spawnng grounds (= R ), 2) marked and never seen agan (= Mˆ - R ), 3) unmarked and nspected on the spawnng grounds (= C - R 4) unmarked and never seen (= N ˆ - Mˆ - C + R ). where, M = the number of fsh tagged at a trap ste, and ), and Nˆ s the populaton estmate. A random sample of sze Nˆ was drawn wth replacement from the emprcal probablty dstrbuton. Values for the * statstcs M, R, and C were calculated and a new populaton sze Nˆ estmated. Ths process was repeated 1,000 tmes to obtan samples for estmates of varance, bas and bounds of 95% confdence ntervals. Varance was estmated by: B Â ˆ * b= 1 v( N ) = 2 ( ˆ * ˆ * N ( b) - N ) B -1 where B equals 1,000 (the number of bootstrap samples). The 95% confdence ntervals of the estmate are taken as +/- 1.96*s( N ) from the bootstrap smulaton. The 95% relatve precson of the estmate s thus 1.96*s( N )/ Nˆ. * ˆ To estmate the statstcal bas, the average or expected bootstrap populaton estmate was subtracted from the pont estmate (Mooney and Duvall 1993:31). * ˆ Bas ˆ = ˆ - ˆ, * ( N ) N N Umpqua Cumulatve Progress Report doc

14 where Nˆ * B Â b= = 1 Nˆ B * ( b) Age and Sex Composton Analyss If a populaton estmate was not stratfed by sze or sex, the proporton of chnook at age from the scale analyss s used to estmate the number of chnook at age for the populaton. The varance was a smple varance of a product: [ ( p ) Nˆ 2 + ( Nˆ 2 var ˆ var ) pˆ var( Nˆ ) var( pˆ )] var( N ) = Â - If a mark-recapture experment was stratfed by sze or sex, then to estmate the age composton of the whole populaton the followng equatons are used: p j =n j /n where n = the number sampled from stratum n the mark-recapture experment n j = the number sampled from stratum that belong to age group j p j = the estmated fracton of the fsh n age group j n stratum v[p j ]= p j (1-p j )/(n -1) The estmated abundance of age group j n the populaton (N j ) s: N j = (p j N ) Where N = the abundance n stratum of the mark-recapture experment. v[n j ] = (v[p j ]N 2 +v[n ]p j 2 -v[n j ]v[p j ]) The estmate fracton of the populaton that belongs to age group j (p j ) s : p j = N j /N where N= N. v[p j ] = v[p j ]{n /N} 2 + (v[n ] (p j -p j ) 2 /N 2 Umpqua Cumulatve Progress Report doc

15 Rado Telemetry Rado telemetry nformaton was used to partton the basn wde mark-recapture estmate nto multple geographc strata. Several assumptons must be taken nto consderaton n order to effectvely use telemetry data: 1. fsh tagged are typcal of the populaton of nterest, and 2. behavor s not altered by handlng or the presence of a tag, and 3. survval s not altered by handlng or presence of a tag. Fsh were selected by a systematc random sample over the entre run durng capture actvtes on all rver systems, whch mnmzed any bas n selecton of tagged fsh (Assumpton 1). From the mark-recapture experment, data on selectvty of fsh ether by sze, sex, or tmng was avalable to assess any bas n the taggng procedure f t exsts. The populaton of nterest s the dstrbuton of tagged fsh wthn the rver basn and above the frst capture ste, snce ths s the only nformaton the mark-recapture estmate wll be usng. Devatons n the expected behavor of handled chnook has been noted by several authors, Bernard et al. (2000) found that there are handlng nduced behavor changes, but dd not estmate any dfferences n the spawner dstrbuton, only a change n mgratory rates (Assumpton 2) Changes n survval between tagged and non-tagged fsh (Assumpton 3) were assessed by anecdotal nformaton gathered at the taggng stes and on the spawnng grounds. The fracton of chnook located n each stratum (trbutary or manstem) was estmated by (Cochran 1977): n pˆ =, where nˆ nˆ = N - n - n - n - n, and h f m l n = number of fsh wth transmtters that spawned n ether a trb. or manstem statum, n h = fsh wth transmtters returned from anglers, n f = fsh wth transmtters that dd not contnue mgratng, n m = fsh wth transmtters that ded before spawnng, and n l = transmtters that were regurgtated, batteres faled, or not recorded agan. The estmated varance of p s: var( pˆ ) = pˆ (1 - pˆ ) nˆ -1 Therefore the estmated number of chnook ( Nˆ ) n each stratum s: Nˆ = pˆ Nˆ, where Nˆ = the chnook salmon escapement estmate from the mark-recapture experment. The varance of the estmated chnook populaton n stratum s (Goodman 1960): [ ( p ) Nˆ 2 + ( Nˆ 2 var ˆ var ) pˆ var( Nˆ ) var( pˆ )] var( N ) = Â - Umpqua Cumulatve Progress Report doc

16 Creel Analyses of In-Rver Harvest The creel surveys were stratfed by month, catch area, and angler type (shore or boat). Dependng on harvest rates, anglers could be further post-stratfed nto prvate trps and guded trps. Data analyss procedures for poststratfcaton of prvate and guded trps wll follow Bernard et al. (1998) f harvest rates dffer sgnfcantly between the trp types. Mssng data ponts from surveyor llness or equpment falures were treated as random events and removed from the samplng frame. Bernard et al. (1998) descrbes several other events whch must be taken nto account durng analyss that can bas harvest estmates ncludng 1) zero ntervews, but anglng effort was counted, 2) zero harvest rate, but effort was counted, and 3) very low (1-2) numbers of ntervews but wth harvest. If any of these stuatons are encountered and deemed to bas the data-set, the data wll be treated as mssng data ponts and the substtuted values derved from methods descrbed n Bernard et al. (1998). Rovng-Access Survey: Harvest was determned separately for kept fsh and for released fsh. Estmated harvest per sample day n a partcular stratum s (Pollock et al. 1994, Bernard et al. 1998): H ˆ ˆ = Ecpue, where: denotes samplng days, Ê = estmated effort, and c pue =average catch per unt. Because the rovng-access surveys only ntervew completed angler trps, average catch per unt effort s estmated as the rato of means (Hoeng et al. 1997): cpue = m  k= m hk 1, where,  k= 1 e k k denotes ndvdual anglers, m denotes the number of anglers ntervewed, h s the number of fsh caught durng fshng trps that were ntervewed, and e s the length n hours of fshng trps of ntervewed anglers. Varance of cpue s estmated as (Bernard et al. 1998): m  k= 1 v( cpue ) = 2 e m 2 ( h - e cpue ) k k ( m -1). Umpqua Cumulatve Progress Report doc

17 Fsh harvested per catch/month strata equals: Hˆ d  Hˆ = 1 = D d where, d = number of sampled days n stratum, and D = total avalable samplng days n stratum. Daly effort s estmated as: Eˆ r  x t= 1 = T r t where, x t denotes the ndvdual rovng count of anglers at tme t, r = number of pressure counts per day, and T = the length of the samplng perod (usually day length). Snce effort s determne systematcally and not randomly the varance equaton s (Wolter 1985): r 2 Â( xt - x( t-1) ) ˆ 2 t= 2 v( E ) = T 2 r ( r -1). The varance of the daly harvest s (Goodman 1960 as cted by Bernard et al. 1998): 2 2 v( Hˆ ) = Eˆ ( cpue ) + cpue v( Eˆ ) - v( cpue ) v( Eˆ and the varance for each catch/month stratum s: ), ˆ s1 v( H ) = D( D - d ) d s 2 1 =  ( Hˆ - Hˆ ) 2 2. d -1 + D d d  = 1 v( Hˆ ), where Total harvest s the sum of all catch n each strata and the total varance of the catch s the sum of all strata varances (Pollock et al. 1994). Umpqua Cumulatve Progress Report doc

18 Rovng-Rovng Surveys: The only dfference n estmaton between the rovng rovng survey and the rovng access survey s the catch per unt effort (cpue) estmator. Wth rovng surveys anglers are ntervewed that have not completed fshng and the mean of ratos estmator should be used (Pollock et al. 1994). cpue m hk  k= ek = 1, where, n k denotes ndvdual anglers, m denotes the number of anglers ntervewed, h k s the number of fsh caught for an ntervewed angler, e k s the length n hours fshed for an ntervewed angler, and n s the number of ntervews for each day. The varance s calculated as (Jones et al. 1995): v( cpue ) Ê m hk  ek Á k= 1 = Ë ek m m  = 1 - cpue e k ˆ 2. RESULTS Spawner Escapement Estmates Umpqua basn fall chnook spawner abundance estmates have become ncreasngly precse over the fve years of the study. In each case, we have presented a fully pooled Peterson estmate as our spawner escapement estmate. Table 3 presents a summary of escapement estmate, precson and bas for each year of ths study. Table 4 presents escapement estmates stratfed by length and sex, and a Darroch estmate stratfed by locaton or tme. Each of these estmates was wthn 10% of the correspondng fully pooled Peterson abundance estmate, therefore we present the fully pooled estmate as ths provdes the best precson. Results of ch-square tests of assumptons of equal mxng of marked and unmarked fsh n tme and space are presented n Appendx B The 1998 feld season was funded as a feasblty study of mark-recapture technques to assess escapement estmates. Sxty fve adult fall chnook were marked at the Happy Valley wer from October 2 through November 3, 1998 (Fg. 2), and 111 carcasses were nspected on spawnng grounds. Fve carcasses were recaptures of marked ndvduals, leadng to a spawnng escapement estmate for the South Umpqua of 1,232 adult fall chnook. The 95% relatve precson was estmated at 105% through bootstrappng. The low precson results from the overall low numbers of chnook salmon marked and carcasses recovered on spawnng grounds durng ths feasblty study, and partcularly from the low number of recaptures of marked fsh. No tests for volatons of assumptons of random mxng were performed due to the low number of recaptured fsh. Umpqua Cumulatve Progress Report doc

19 Table 3: Fall chnook spawner escapement estmates wth assocated 95% confdence ntervals, relatve precson and bas estmate for the South Umpqua/Cow Creek subsystem and the full Umpqua basn (2001 and 2002). Bootstrap Smulaton 95% CI Standard 95% Rel Precson Bas % Bas Rel Bas Escapement Estmate Year Mean Standard Devaton CV (s.d.*1.96)/mean (Pld Ptrsn - Btstrp Mn) (Bas/sd) 1232 S. Umpqua % % % S. Umpqua % % % S. Umpqua % % % S. Umpqua % 9.807% % S. Umpqua % % % Full basn % % % Full basn % % % Umpqua Cumulatve Progress Report doc

20 Table 4. Stratfed, fully pooled Peterson and Darroch spawner escapement estmates for Umpqua System (percentages under stratfed estmates and Darroch estmates are relatve to the fully pooled Peterson estmate for that year) Year Sex Sze (mm FL) Marked Carcasses Recaptures Fully Pooled Peterson Estmate Sex-Stratfed Peterson Estmate Sze Stratfed Sze and Sex Stratfed % of marked fsh ultmately recaptured % of carcasses nspected on spawnng grounds that were marked PPE 1998 S. Umpqua 600 < % 4.50% 1999 S. Umpqua all 600 < % 14.84% 94.26% males 600 < % 17.24% females 600< % 14.22% all % 29.41% % 18.05% > % % all > % 19.37% Darroch Estmates 2000 SPACE TIME S. Umpqua all 600 < % 17.28% % 103% 99.41% 99.41% 95% CI males 600 < ( ) 14.17% 14.41% females 600< % 19.29% all % 16.92% % 17.26% % 17.19% Umpqua Cumulatve Progress Report doc

21 Table 4. contnued Darroch Estmates 2001 SPACE TIME S. Umpqua all 600 < % 24.43% % 95.50% males 600 < % CI 15.14% 21.99% ( ) females 600< % 26.89% Umpqua entre basn all 600 < % 1.71% % 17.14% 3.45% > % 1.45% males all 600 < females all 600< Darroch Estmates 2002 SPACE TIME S. Umpqua All Sum> % 10.86% <600 mm % 99.44% % % % 6.15% 4.88% % 9.18% % 11.10% % 13.10% Males Sum> % 12.03% <600 mm % 5.00% % 11.01% % 11.93% % 13.87% Females Sum> % 9.39% <600 mm % 0.00% % 5.15% % 10.48% % 7.69% 2002 Umpqua entre basn All >600 mm % 1.53% % % % 7.37% 1.12% Umpqua Cumulatve Progress Report doc

22 Table 4. contnued % 1.48% % 2.53% >600 mm % 1.75% % 1.17% % 1.63% % 2.90% >600 mm % 1.25% % 1.02% % 1.36% % 0.00% Umpqua Cumulatve Progress Report doc

23 1999 We estmated that 1,980 adult fall chnook spawned n the South Umpqua/Cow Creek subsystem above the markng ste n Frst capture and markng of Umpqua fall chnook took place at Happy Valley wer through the month of October n 1999 (Fg. 2). Carcass counts on spawnng grounds, and nspecton of carcasses for marks took place from md-october through the end of November Fsh marked and carcasses nspected on spawnng grounds ncreased nearly four-fold relatve to Recaptures of marked fsh on the spawnng grounds ncreased by a factor of 12. Unsurprsngly, the spawner escapement estmate was larger. More mportantly, the 95% relatve precson of our spawner escapement estmate s 21.7% whch meets the project objectve (Tables 3 and 4). Based on ch square analyss of spatal and temporal dstrbuton of tagged vs nontagged and male vs female chnook, the null hypotheses that all fsh mx randomly was not rejected. (Appendx B) We estmate 2,697 adult fall chnook spawned above the Happy Valley wer capture ste n the South Umpqua/Cow Creek subsystem n All stratfed estmates were wthn 10% of the fully pooled Peterson estmate. The 95% relatve precson of the estmate s 16% as estmated from boostrappng. A feasblty study to develop a full-basn mark-recapture spawner estmate (ncludng the manstem above tdal nfluence, the North Fork Umpqua, and the South Fork manstem below the Happy Valley trap) was ntated n Thrty seven chnook salmon were captured n tangle nets, prncpally at RM 29.5 (Fg. 2). However, 70 coho salmon were captured and released. Intal daytme nettng efforts were shfted to the nght due to observed nght avodance. Soak tmes at nght vared dependng on the number of coho captured. No basn-wde estmate was developed as only two fall chnook marked n manstem taggng operatons were recovered on spawnng grounds. Frst capture and markng of adult fall chnook salmon at the Happy Valley trap on the South Umpqua was hghly concentrated n the month of October (Fg. 2). A total of 739 chnook salmon were captured and examned for marks from earler nettng. Of these, 469 adult fall chnook salmon (240 males and 229 females) were marked and released to contnue upstream. Carcass recovery n the South Umpqua and Cow Creek extended from md-october through the frst week of December. A total of 606 carcasses (573 of adult sze, >600 mm fork length) were nspected for marks; 99 adult szed marked fsh were recaptured. Only two of the fsh recaptured had been marked durng manstem nettng operatons. Ch-square analyss of the dstrbuton of carcass recoveres by sex and by tme (early or late) ndcated that the null hypothess of random mxng could not be rejected. However, ch-square analyss of carcass dstrbuton between the South Umpqua and Cow Creek reveals that a dsproportonate number of marked fsh were found n Cow Creek where 20% of the carcasses nspected bore marks, whereas only 14% of nspected carcasses n Umpqua Cumulatve Progress Report doc 23

24 the South Umpqua were marked (Appendx B). However, the Darroch stratfed estmator of spawner abundance was 99.4% of the estmate developed by the pooled Peterson model We estmate the fall chnook spawner abundance for the entre Umpqua basn, ncludng the South Umpqua basn above Happy Valley trap, was 6,612 n Ths estmate was based on 1,344 adult carcasses that were nspected for marks that ncluded 23 recaptured marked fsh. Not ncluded n ths estmate were 206 chnook that were observed crossng Wnchester Dam, two of whch were marked. The spawner escapement estmate for the South Umpqua/Cow Creek porton of the system was 5,402 based on 958 adult carcasses nspected for marks, and 234 recaptured fsh. The 95% relatve precson of these estmates are 9.8% and 38.3% for the South Umpqua sub-basn, and the full Umpqua basn, respectvely. (Tables 3 and 4). A total of 116 adult chnook (> 600 mm FL) and 53 jack chnook were captured, tagged wth anchor tags and released n the lower manstem Umpqua between July 31 and October 2, 2001 (Fg. 2). Thrty one adult chnook salmon had analog esophageal rado transmtters mplanted. At Happy Valley trap, 1,704 chnook were examned for marks, of whch 238 were taken for brood, 1,466 were marked and released. Nne percent (9%) of the chnook marked and released at Happy Valley trap were jacks (<600 mm FL). Eght-sx percent (86%) of the chnook were captured n a three-week perod (October 7 to October 27), wth a peak weekly count of 827 chnook the week of October 21 (Fg. 2). The sex rato at the trap s slghtly skewed towards males (900 males, 804 females). Thrteen marked fsh from event 1 were recovered at the trap ste. Eleven of the marked fsh had retaned ther numbered anchor tag. The remanng two were dentfed by the secondary mark: the left operculum marks on all 13 fsh had grown over but were vsble due to coloraton dfferences from the unpunched operculum. In addton, 879 coho were captured and released. Extreme flows (hgh or low) can have an adverse effect on the catchablty of mgratng chnook at the Happy Valley trap. In 2001, trappng at Happy Valley was hampered by large amounts of aquatc vegetaton that weghed down the floatng wer and allowed chnook to avod the trap. Extremely low summer flows and hgh water temperatures throughout the South Umpqua Basn are thought to be the catalyst for ths dense vegetaton growth. Durng the frst three weeks of trap operaton, mantenance of the wer durng daylght hours resulted n only three to sx hours of trap operaton. Spawnng surveys were conducted from October 14 through November 24, Spawnng surveys nvolved floatng each reach wth two catarafts. Water condtons through November 10 were deal for spawnng surveys, low water wth hgh vsblty. From November 10 to November 24 hgher flows wth ncreased turbdty reduced vsblty on all spawnng surveys. Umpqua Cumulatve Progress Report doc 24

25 Ch-square tests of the assumptons of random mxng of marked and unmarked fsh and of males and females n the South Umpqua basn allow us to accept the null hypothess of equal mxng (Appendx B) 2002 We estmate the fall chnook spawner abundance for the South Umpqua/Cow Creek subsystem as 10,477 adult fall chnook. The 95% relatve precson as estmated through bootstrappng s 10.2%. Stratfed Peterson estmates (by sze and/or sex) and ndependent Darroch estmates of spawner escapement numbers were all wthn 3% of the fully pooled Peterson estmate. We estmate the fall chnook spawner abundance for the entre Umpqua basn as 13,064 based on thrty sx recaptures of adult fall chnook on spawnng grounds that were orgnally marked at Famly Camp. Stratfed estmates were wthn 10% of ths fgure. The 95% relatve precson of ths estmate s 31.4% We also developed an alternatve estmate from the number of fall chnook nspected, and recaptures observed, at the Happy Valley wer ste. Usng ths method, 21 adult recaptures of 1380 fsh nspected results n a basn-wde pooled Peterson estmate of 12,867 adult fall chnook. The precson of ths alternatve estmate would be correspondngly lower than that descrbed above because of the lower numbers of fsh nspected for marks and of recaptures (Tables 3 and 4). Crews conducted tangle nettng at Rver Mle 29.5 (Famly Camp) from 7 August through 24 September 2002 (Fg. 2). Two hundred four adult sze fall chnook (>600 mm fork length) were captured, marked wth an operculum punch and axllary clp, and released. Seventy two of these fsh receved an esophageal mplant of a rado transmtter. At the Happy Valley trap, 1380 adult sze fall chnook were handled and nspected for marks from Famly Camp nettng. Twenty-one adult fall chnook marked at Famly Camp were recaptured. Approxmately 165 adult fsh were retaned for broodstock. 1,141 adult fall chnook receved an addtonal operculum punch and were released above the wer, thus becomng the marked populaton for the South Umpqua/Cow Creek porton of the mark-recapture experment. Carcass recovery on spawnng grounds n the South Umpqua/Cow Creek subsystem took place from October 4 through the end of December ,465 carcasses were recovered and nspected for marks, of whch 2,357 were of adult sze and had ntact opercula (1,313 males and 1,044 females). Of these, 256 were recaptures of chnook ntally marked at the Happy Valley wer and 36 were recaptures of chnook ntally marked at the Famly Camp nettng ste. Age and Sex Composton Reconstructon Age and sex composton of the South Umpqua fall chnook runs are presented n Table 5. We do not yet have scale data from the 2002 feld season. Age dstrbuton of males was strongly weghted toward age 3 ndvduals (approxmately 65%) wth most of the rest age 4. Age 5 and 6 males are unusual n our study. (n.b. Our study s largely exclusve of jack males that make up an apprecable number of returnng Umpqua Cumulatve Progress Report doc 25