Clearwater MPG Snake River Steelhead DPS

SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Following pages are an analysis of ongoing monitoring programs in the MPG by TRT identified population, an evaluation of the quality of the information, and an evaluation of what would be needed to improve the monitoring and to move toward meeting NOAA Fisheries Service monitoring guidance standards.

Evaluations shown in this document are drawn from the work completed by the Columbia River Fish and Wildlife Authority through A. Byrne (IDFG) and C. Beasley et al. of the Collaborative System-wide Monitoring and Evaluation Project and through direct participation of the fish co-managers and FCRP action agencies.

This evaluation is a result of a workshop held at IDFG on March 17 in Boise, and includes edits provided by:

 Alan Byrne, IDFG, 4/1/09  Jay Hesse, NPT,  Lytle Denny, SBT and  Ed Murrell, NOAA. Page 2 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

MPG Population Primary Desired Monitoring Needed Current Data Quality & Data RPA Eligible Agency Indicator Certainty Monitoring Certainty Improvement Proposed Projects Actions Needed

Clearwater MPG Adult 1990-055-00 IDAHO  The IC-TRT was  GSI pilot study 50.5 Abundance, STEELHEAD M&E unable to make initiated in 2008 for B run  Implement the General STUDIES Adult any adult adults at LGR will genotyping of all  Estimates wild Productivity, abundance assess level of hatchery spawners adult steelhead so Parental Based and other VSP estimates for any resolution. It is escapement and Tagging (PBT) criteria population. anticipated that age structure techniques can be  Unlikely to get adults can be used. passing Lower MPG or assigned at the Granite Dam population scale population or  COE counts at adult abundance watershed scale.  Design and Lower Granite data using  Review, summarize, implement a smolt Dam provide a sampling program at traditional and synthesize data good estimate of Lower Granite Dam the total number methods (redd by population to estimate the of hatchery and counts or weirs)  Use PBT to identify number of smolts wild steelhead  Much of the GSI hatchery origin and the age adults for the data collected adults at Lower composition from entire DPS. each population have yet to be Granite Dam and in  Natural-origin using GSI and scale synthesized at the tributaries. Snake River analysis. Steelhead population level Snake River steelhead abundance  Estimates of annual run- reconstruction of estimated at natural origin  Transition from Lower Granite hatchery and wild steelhead adult microsatellite to Dam (LGR) using incidental returns, harvest, and SNP’s technology for Genetic Stock mortality from escapement to known Identification (GSI) sport fisheries are and unknown GSI and PBT analysis. began in 2008 imprecise. population areas $150K/yr (ISMES). Collect adult life  Estimating adult history data at the Age composition  Analyze adult and steelhead population scale. and sex ratios also abundance cannot juvenile tissue determined.  Develop alternative be done samples collected by  IDFG estimates methods to estimate accurately using IDFG and Tribes for steelhead harvest traditional spatial distribution inclusion in baseline in recreational methods in high  Develop surveys of genetic database Page 3 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

fisheries using a and turbid flows, hatchery spawner using SNP’s. telephone survey juvenile estimates fraction in index (only hatchery are important as a streams origin adipose proxy for adult  Implement a 5-year clipped fish may productivity .  Genetic baseline rotating panel to be kept). needs to be collect genetic  Estimates of tribal maintained at regular samples to maintain harvest (hatchery intervals an d update baseline and unmarked)  Refine genetic database supported by characterization of A- LSRCP evaluation run and B-run contract and BPA populations based on IDFG BiOp Accord 200206000 population specific proposes to increase B  ISMES (BPA data. Run monitoring in 199005500 )  Validation of Clearwater and Salmon $784K/yr unmarked hatchery river drainages. To meet RPA 50.5. BPA production  INPMEP (BPA contract 199005500 199107300) identification by fin $785K/yr shape or estimates of Snake River steelhead  BPA 200500200 origin by other annual run- 39013 $250,853 methods. reconstruction of hatchery and wild  Determine the returns, harvest, and encounter rate of escapement to known natural adult and unknown steelhead and the population areas mortality rate of  Estimate natural released adult population incidental steelhead in mortality from sport recreational fisheries fisheries.  NPT proposes to install PIT tag arrays  Investigate Genetic in South Fork Parentage Analysis Clearwater River to Page 4 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Techniques to utilize proposed PIT- Estimate Spawner tagging by ISMEP Abundance in ESA- project listed Steelhead Populations by sampling juveniles (methods outlined in unfunded BPA proposal 200732300)

Clearwater Adult Annual population- Natural-origin Spawner Abundance  Hatchery fish Potlatch River is Snake River steelhead Abundance level estimates released at intensively monitored annual run- Lower and has good data reconstruction of with a CV value on Kooskia Hatchery Mainstem quality starting in 2006 hatchery returns, average of 15% or (Clear Creek) and A Run Clear Creek has longer harvest, and less. Dworshak term index data, no escapement to known National Fish mark-recapture and unknown Power analysis Hatchery for Accuracy of GSI to population areas (new) calculated for harvest identify this population Include PIT tag arrays needs to be in Potlatch and Lapwai data? augmentation. determined. Creek in ISEMP study  Four temporary No CV estimates design. weirs (Big Bear, Little Bear, West Fork and East Fork) operated by IDFG count steelhead using mark recapture in the Potlatch drainage (IMW).  One hatchery weir on Clear Creek operated by Page 5 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

USFWS/NPT for Chinook is not efficient during high flows (operation not planned for 2009).  Potlatch River has been designated as an Intensively Monitored Watershed (IMW) by IDFG and is being treated for improved instream structure, channel diversity, and other habitat improvements. NOAA Funded PCSRF Contract $187K/yr  Natural-origin Snake River Steelhead MPG and population abundance via Genetic Stock Identification (GSI) at Lower Granite Dam began in 2008 $150K/yr Page 6 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

(ISMES)  ISEMP Adult PIT Tagging may enable PIT Tag arrays in Potlatch and Lapwai Creeks make escapement estimates in these streams. Clearwater Adult Adult/Adult ratio  Sex ratio  Age structure  Need better  Develop surveys RPA 50.7 Productivity with low σ2 Lower  Hatchery % information, sex estimates of of hatchery ratios, hatchery natural cohort age spawner fraction Mainstem  Cohorts and sex structure percentage in index streams A Run  Harvest estimated at IMW  Estimates of natural population  Reevaluate weirs incidental juvenile sampling  Hatchery mortality from design and verify percentage recreational age structure estimated at IMW fisheries are assumptions PIT tag arrays imprecise. needed for  Estimating adult  PIT-tags scanned productivity steelhead estimates at IMW weirs abundance cannot however, sample be done  Develop habitat size is too small accurately using and life cycle for precise current methods model(s) to estimates in high and turbid synthesize flows, juvenile available data to  IDFG Accord estimates are extrapolate from provides important as a $150,000/yr to do proxy for adult index samples to GSI assessments productivity . an appropriate (combined with population scale. age and sex Page 7 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

comp.) in Clearwater and Salmon River.  IDFG phone survey estimates sport harvest in recreational fisheries.  Sport fishing for adult steelhead within population boundaries is permitted in mainstem Clearwater River and MF Clearwater (to Clear Creek) only.  Annual parr density monitoring (surrogate for adults) conducted by IDFG within population BPA 199107300  Intensively Monitored Watershed (IMW) Project, NOAA Funded PCSRF Contract Page 8 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

$187K/yr  ISMES (BPA 199005500 ) $784K/yr

Clearwater Juvenile Annual population-  Juvenile Migrant Abundance  Two screw traps  Short time frame  Increased PIT IMWs Potlatch and Productivity level estimates Lemhi River Lower  Smolt/Adult ratio and two PIT tag for Potlatch trap tagging or roll up with a CV value on NOAA – PSMFC Mainstem arrays operated data SARs to larger average of 15% or  Juvenile Survival funding $392,000 by IDFG in upper  Representativenes scale A Run less.  SARs IDFG Potlatch River s of Potlatch to  Explore (IMW). entire population alternative Power analysis Explore feasibility of  One screw trap in  Imprecision of method of calculated for using GSI and age Clear Creek SARs at estimating SARs data? comp. for smolts at (USFWS/NPT) population level with precision LGR operated 2-3  Determining months mainly for “what is a smolt” Chinook. ISS trap is very important. planned to cease What are the operation in 2014. rates of  PIT tagging occurs residency? What throughout proportion of the Potlatch drainage fish captured and using a variety of tagged at screw capture methods traps are smolts (IMW). Used for and/or actively juvenile survival migrating? and SARs  No Trap CV  Juvenile migrant estimates abundance estimated at all screw traps using mark recapture Page 9 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

(IMW, ISS)  Survival of juveniles (within basin and to LGR) estimated using PIT tags (IMW)  Age structure estimated from scale analysis at all screw traps (IMW, ISMES)  In 2007 IDFG adopted a rotating panel probabilistic GRTS design for assessing the abundance of juvenile salmonids (INPMEP, BPA#1999107300) , Potlatch done in 2008  Intensively Monitored Watershed (IMW) Project, NOAA Funded PCSRF Contract $187K/yr  NPT estimating Page 10 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Juvenile density and distribution using GRTS design in all tributaries except Potlatch and Clear Creek (BPA 200723300). Single year estimates.  ISMES (BPA 199005500 ) $784K/yr  INPMEP (BPA 199107300) $785K/yr Clearwater Spatial Periodic  Adult redd distribution  In 2007 IDFG  adult spawner Develop alternative Distribution distribution adopted a rotating distribution methods to estimate Lower  Juvenile parr distribution spatial distribution estimates with panel probabilistic limited to Potlatch Mainstem (e.g., fry surveys, radio ability to detect a GRTS design for  Inference of and acoustic tagging) A Run 15% change with assessing the spawner 80% certainty. abundance of distribution from juvenile salmonids parr is uncertain (INPMEP,  Extensive parr BPA#1999107300) distribution data , Potlatch done in for Potlatch River 2008 but reducing drainage from scope in future. IDFG  NPT estimating electrofishing juvenile density surveys (2003- and distribution 2008) using GRTS design in all tributaries Page 11 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

except Potlatch and Clear Creek (BPA 200723300). Single year estimates.  Juvenile distribution estimated in Lapwai, Big Canyon, and Lawyers creek by NPT yearly.  Intensively Monitored Watershed (IMW) Project, NOAA Funded PCSRF Contract $187K/yr  ISMES (BPA 199005500 ) $784K/yr  INPMEP (BPA 199107300) $785K/yr Clearwater Species  Short term  Age  Genetics samples   Genetic baseline 5-year rotating panel Diversity for baseline genetic Lower collection of  Sex ratios from Upper and Representativenes needs to be phenotypes Lower Potlatch s of index streams maintained at samples (ISMES) Mainstem  Size River adults being  Long term to entire regular intervals A Run  Cohort structure analyzed annually collection of at IDFG Eagle Lab population  Develop habitat genotypes  Run Timing (IMW) and life history  DNA  There appear to model(s) to Page 12 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

be sufficient synthesize samples being available data to collected to extrapolate from provide good index samples to baseline for future ESA status review an appropriate of genetic population scale. diversity. Since 2000, Idaho Steelhead Monitoring and Evaluation Studies (ISMES) has collected tissue samples from populations across all the various populations in the Clearwater and Salmon basins  In 2007 678 genetics samples across Idaho were analyzed  Juvenile and adult life history characteristics estimated at weirs and screw traps (i.e., scales, lengths, PIT tags, gender).  ISMES (BPA 199005500 ) $784K/yr Page 13 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Clearwater  HGMP  PNOS  Funded under Integrate wild Implement genotyping implemented LSRCP steelhead monitoring of all hatchery Hatchery  PHOS at Red and Crooked spawners so PBT can  All steelhead IDFG  Marked  Rivers with state-wide used to identify parr, DNA released offsite at Product monitoring program. smolts, and adults. SF Clearwater Evaluate  Supplementat River satellite supplementation ion facilities, directly releases. monitoring into the SF Clearwater River,  Genotype/ and Lolo Creek. phenotype  Hatchery estimates smolt- to-adult survival rate (SAR) for transported and in-river wild and hatchery stream type Chinook and steelhead under LSRCP and BPA contract #199602000  Adult returns, kelts and ages at Red River and Crooked River satellite hatchery racks  No hatchery steelhead releases at Powell satellite facility (used for Chinook only) Page 14 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Dworshak National  HGMP  PNOS  Built to mitigate Implement genotyping Fish Hatchery of all hatchery implemented  PHOS for the loss of USFWS steelhead spawners so PBT can  Marked  DNA production used to identify parr, Product upstream of smolts, and adults  Supplementat Dworshak Dam. ion  Funded under monitoring LSRCP  Genotype/  Most of the smolts are phenotype released at Dworshak Hatchery and Kooskia Hatchery.  Hatchery estimates smolt- to-adult survival rate (SAR) for transported and in-river wild and hatchery stream type Chinook and steelhead under LSRCP and BPA contract #199602000  Sex, length, genetic samples collected from adult returns to hatchery rack. Page 15 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Kooskia National  HGMP  PNOS  Located on Clear Address hatchery Improve operation of Implement genotyping Fish Hatchery steelhead releases weir for steelhead of all hatchery implemented  PHOS Creek upstream of USFWS/NPT the confluence relative to monitoring (e.g., debris cleaning, spawners so PBT can  Genotype/  DNA with the Middle natural steelhead. mark-recapture, stray used to identify parr, phenotype Fork Clearwater rate). smolts, and adults River  Raises and collects spring Chinook only. Release site for hatchery steelhead smolts reared at Dworshak NFH.  Funded under LSRCP  Sex, length, scales, and genetic samples collected from adult returns to hatchery weir. SF Clearwater Adult Annual population- Natural-origin Spawner Abundance  Hatchery fish Do not evaluate mark- Snake River steelhead RPA 50.5  IDFG BiOp Accord Abundance level estimates released for recapture at hatchery annual run- proposes to River weirs. Do not collect reconstruction of with a CV value on supplementation increase B Run B Run kelts. Weirs designed hatchery returns, average of 15% or and harvest for Chinook and not harvest, and monitoring in less. augmentation. efficient at high flows escapement to known Clearwater and  Two hatchery Both weirs upstream and unknown Salmon River Power analysis weirs operated by and only intercept a population areas drainages. To calculated for small portion of Integrate wild IDFG count meet RPA 50.5. population steelhead monitoring data? BPA contract steelhead using Accuracy of GSI to at Red and Crooked 199005500 mark recapture in identify this population Rivers with state-wide Crooked and Red needs to be monitoring program. $150k/yr River. determined. Investigate Genetic Snake River steelhead No CV estimates made Parentage Analysis annual run-  Natural-origin Techniques to Estimate reconstruction of Page 16 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Snake River Spawner Abundance in hatchery returns, Steelhead MPG ESA-listed Steelhead harvest, and and population Populations escapement to known (200732300) and unknown abundance via population areas (new) Genetic Stock Identification (GSI) at Lower Granite Dam began in 2008 $150K/yr (ISMES)

SF Clearwater Adult Adult/Adult ratio  Sex ratio  Age structure  Need better  Develop surveys RPA 50.5  IDFG BiOp Accord 2 Productivity with low σ information, sex estimates of of hatchery proposes to increase River  Hatchery % RPA 50.7 ratios, hatchery natural cohort age spawner fraction B Run monitoring in B Run  Cohorts and sex structure percentage in index streams Clearwater and  Harvest estimated at weirs  Population is Salmon River heavily influenced  Reevaluate drainages. To meet  PIT-tags scanned by hatchery juvenile sampling at weirs however, steelhead; design and verify RPA 50.5. BPA sample size is too hatchery fraction age structure contract 199005500 small for precise data are lacking. assumptions $150k/yr estimates of adult  Estimates of needed for  NPT proposes productivity natural population productivity supplementation incidental estimates effectiveness  IDFG Accord mortality from monitoring in SF provides recreational  Develop habitat $150,000/yr to do fisheries are and life cycle Clearwater. GSI assessments imprecise. model(s) to (combined with Estimating adult synthesize age and sex steelhead available data to abundance cannot comp.) in extrapolate from be done Clearwater and accurately using index samples to Salmon River. current methods an appropriate in high and turbid population scale. Page 17 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

 IDFG phone flows, juvenile  Need survey estimates estimates are supplementation important as a sport harvest in effectiveness proxy for adult recreational productivity . monitoring fisheries.  Sport fishing for adult steelhead within population boundaries is permitted in mainstem SF Clearwater River only.  Annual parr density monitoring (surrogate for adults) conducted by IDFG within population BPA 199107300  ISMES (BPA 199005500 ) $784K/yr SF Clearwater Juvenile Annual population-  Juvenile Migrant Abundance  IDFG /NPT   Increased PIT YES Explore feasibility of Productivity level estimates RPA 50.5 using GSI and age River  Smolt/Adult ratio operates 3 screw Representativenes tagging or roll up with a CV value on traps, in s of index streams SARs to larger comp. for smolts at B Run  Juvenile Survival average of 15% or American, to entire scale LGR less.  SARs Crooked and Red population  Explore  rivers (ISS,  Imprecision of alternative Power analysis 198909800, all SARs at method of Page 18 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

calculated for scheduled to population level estimating SARs data? cease operation in  No CV estimates with precision 2014). made  NPT operates 1 screw trap in Newsome Creek, BPA # 198335003  Juvenile migrant abundance estimated at screw traps using PIT Tag mark recapture (ISS 198909800)  Survival of juveniles to LGR estimated using PIT tags  Age structure estimated from scales collected at screw traps  In 2007 IDFG adopted a rotating panel probabilistic GRTS design for assessing the abundance of juvenile salmonids (INPMEP, BPA#1999107300) Page 19 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

 ISMES (BPA 199005500 ) $784K/yr  INPMEP (BPA 199107300) $785K/yr

SF Clearwater Spatial Periodic  Adult redd distribution  In 2007 IDFG  No data on adult  Develop Distribution distribution River  Juvenile parr distribution adopted a rotating spawner alternative estimates with B Run panel probabilistic distribution methods to ability to detect a GRTS design for  Inference of estimate spatial 15% change with assessing the spawner distribution (e.g., 80% certainty. abundance of distribution from fry surveys, radio juvenile parr is uncertain. and acoustic salmonids. tagging) Crooked River done in 2008 and will be repeated. (INPMEP (BPA 199107300) $785K/yr)  NPT estimating Juvenile density and distribution using GRTS design in all tributaries up to Butcher Creek (BPA 200723300). Single year estimates.  ISMES (BPA Page 20 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

199005500 ) $784K/yr

SF Clearwater Species  Short term  Age  There appear to Representativeness of  Genetic baseline 5-year rotating panel Diversity collection of be sufficient index streams to entire needs to be for baseline genetic River  Sex ratios population phenotypes samples being maintained at samples (ISMES) B Run  Size collected to  Long term regular intervals  Cohort structure provide good collection of baseline for future  Develop habitat genotypes  Run Timing ESA status review and life history  DNA of genetic model(s) to diversity. Since synthesize 2000, Idaho available data to Steelhead extrapolate from Monitoring and Evaluation Studies index samples to (ISMES) has an appropriate collected tissue population scale. samples from populations across all the various populations in the Clearwater and Salmon basins  In 2007 678 genetics samples across Idaho were analyzed  Crooked River adult steelhead Page 21 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

genetics collected and processed at IDFG Eagle Lab (2007-2008)  Juvenile and adult life history characteristics estimated at weirs and screw traps (i.e., scales, lengths, PIT tags, gender).  ISMES (BPA 199005500 ) $784K/yr Lolo Creek Adult Annual population- Natural-origin Spawner Abundance  Hatchery fish Genetic samples not Collect genetic samples RPA 50.5 IDFG BiOp Accord Abundance level estimates released for included in baseline. Investigate Genetic proposes to increase B B Run This is a gap in the Parentage Analysis Run monitoring in with a CV value on supplementation. overall GSI baseline Techniques to Estimate Clearwater and Salmon average of 15% or  No adult database. Spawner Abundance in River drainages. To less. steelhead weirs Supplementation with ESA-listed Steelhead meet RPA 50.5. BPA Dworshak origin Populations contract 199005500  Natural-origin Power analysis hatchery smolts will (200732300) $150k/yr Snake River calculated for increase to 200K per NPT proposes Steelhead MPG data? year in 2010 and may constructing and population confound methods to steelhead/Chinook abundance via estimate natural weir in conjunction Genetic Stock spawners. with increased B-run Identification (GSI) No CV estimates made steelhead supplementation at Lower Granite effectiveness research Dam began in in Lolo Creek ($1,500 K 2008 $150K/yr one-time capital cost (ISMES) for weir and $500/yr for supplementation effectiveness RM&E) Page 22 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Lolo Creek Adult Adult/Adult ratio  Sex ratio  No Lolo Creek  Lacking estimates  Develop habitat RPA 50.5 IDFG BiOp Accord Productivity with low σ2 proposes to increase B B Run  Hatchery % specific data of natural cohort and life cycle age and sex RPA 50.7 Run monitoring in  IDFG Accord model(s) to  Cohorts structure Clearwater and Salmon provides synthesize River drainages. To  Harvest  Population is available data to meet RPA 50.5. BPA $150,000/yr to do influenced by extrapolate from contract 199005500 GSI assessments hatchery $150k/yr (combined with steelhead; other populations. NPT proposes age and sex hatchery fraction  Need to be able to Supplementation data are lacking. comp.) in identify adults effectiveness Clearwater and  Estimates of returning from monitoring of B Run in Salmon River. natural population supplementation SF and Lolo $500,000 incidental  Sport fishing for smolt releases. Nez Perce Tribal mortality from Hatchery Monitoring adult steelhead  Supplementation recreational and Evaluation (NPTH not permitted fisheries are effectiveness M&E M&E) (Lolo Creek within population imprecise. is needed. Permanent Weir) new boundaries.  NPT hatchery structure - Capital monitoring and Construction one time cost. $1,500,000 evaluation weir construction $1,500,000n Lolo Creek Juvenile Annual population-  Juvenile Migrant Abundance  No Lolo Creek  Estimates of smolt  Increase number RPA 50.5 Explore feasibility of Productivity level estimates specific data immigration with of PIT tags using GSI and age B Run  Smolt/Adult ratio comp. for smolts at with a CV value on trap efficiency  NPT operates a  PIT-tag steelhead LGR average of 15% or juvenile screw available. No CV at screw trap. IDFG BiOp Accord less. estimates made trap located at  Scale collection proposes to increase B Area below trap Run monitoring in rkm 21 that for determining Power analysis not considered a Clearwater and Salmon targets Chinook. age structure and calculated for River drainages. To Steelhead are not spawning area for genetic profile meet RPA 50.5. BPA data? steelhead PIT-tagged. contract 199005500 $150k/yr Page 23 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Lolo Creek Spatial Periodic  Adult redd distribution  No Lolo Creek  NPT proposes Distribution distribution B Run  Juvenile parr distribution specific data supplementation estimates with effectiveness study ability to detect a including GRTS 15% change with juvenile distribution and density sampling 80% certainty.

Lolo Creek Species  Short term  Age  No Lolo Creek  Collect data at 5-year rotating panel Diversity for baseline genetic B Run collection of  Sex ratios specific data. screw trap phenotypes samples (ISMES)  Size  Collect samples  Long term for genetic  Cohort structure collection of baseline database. genotypes  Run Timing  DNA

Lochsa River Adult Annual population- Natural-origin Spawner Abundance  No hatchery fish Fish Creek has good Snake River steelhead RPA 50.5 IDFG BiOp Accord data quality starting in annual run- B Run Abundance level estimates released proposes to increase B with a CV value on 1992 reconstruction of Run monitoring in  IDFG operates one It is expected that GSI hatchery returns, average of 15% or Clearwater and Salmon temporary weir will accurately identify harvest, and less. River drainages. To on Fish Creek with this population escapement to known meet RPA 50.5. BPA mark recapture however this must be and unknown Power analysis contract 199005500 estimates that verified. population areas (new) calculated for data No CV estimates made Investigate Genetic $150k/yr provides index for Parentage Analysis population Techniques to Estimate  Natural-origin Spawner Abundance in Snake River ESA-listed Steelhead Steelhead MPG Populations (200732300) and population abundance via Genetic Stock Identification (GSI) Page 24 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

at Lower Granite Dam began in 2008 $150K/yr (ISMES)  ISMES (BPA 199005500 ) $784K/yr Lochsa River Adult Adult/Adult ratio  Sex ratio  Age structure  Need better  Develop habitat RPA 50.5 IDFG BiOp Accord 2 Productivity with low σ information, sex estimates of and life cycle proposes to increase B B Run  Hatchery % RPA 50.7 ratios, hatchery natural cohort model(s) to Run monitoring in  Cohorts percentage structure via GSI synthesize Clearwater and Salmon  Harvest River drainages. To estimated at weir  Population is not available data to meet RPA 50.5. BPA  PIT-tags scanned heavily influenced extrapolate from contract 199005500 at weir however, by hatchery other populations. steelhead; $150k/yr sample size is too  Develop surveys hatchery fraction small for precise data are lacking of hatchery estimates in some except for Fish spawner fraction years Creek.. in index streams  No hatchery fish  Estimates of  Reevaluate stocked into natural population juvenile sampling watershed. incidental design and verify mortality from Hatchery strays age structure recreational are not passed fisheries are assumptions upstream of weir imprecise. needed for in Fish Creek  Estimating adult productivity  Annual parr steelhead estimates density abundance cannot monitoring be done accurately at the (surrogate for population scale adults) conducted using current by IDFG within methods in high Page 25 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

population BPA and turbid flows, 199107300 IDFG juvenile estimates Accord provides are important as a proxy for adult $150,000/yr to do productivity . GSI assessments (combined with age and sex comp.) in Clearwater and Salmon River.  Sport fishing for adult steelhead is not permitted within population boundaries.  ISMES (BPA 199005500 ) $784K/yr Lochsa River Juvenile Annual population-  Juvenile Migrant Abundance  IDFG operates 2  Representativenes  Increased PIT RPA 50.5 Explore feasibility of Productivity level estimates using GSI and age B Run  Smolt/Adult ratio screw traps. O ne s of Fish Creek tagging in other with a CV value on in Crooked Fork SAR estimates to streams or roll up comp. for smolts at average of 15% or and one in Colt entire population SARs to larger LGR less. Killed (ISS,  Dispersed PIT scale IDFG BiOp Accord 198909800,. tagging conducted  Explore Power analysis proposes to increase B These traps will in Lochsa alternative calculated for Run monitoring in cease operation in tributaries 1993- method of data? Clearwater and Salmon 2014) 2006 (199107300) estimating SARs River drainages. To  IDFG operates 1 FISH CREEK has meet RPA 50.5. BPA screw trap in Fish precise estimates contract 199005500 Creek , BPA because sample $150k/yr 199005500 size is large Page 26 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

 Age structure enough. This is estimated from the best we have scale analysis (and the Imnaha River)  Juvenile migrant abundance  No CV estimates estimated at have been screw traps using provided for this mark recapture analysis (ISS, ISMES)  Survival of juveniles to LGR estimated using PIT tags  In 2007 IDFG adopted a rotating panel probabilistic GRTS design for assessing the abundance of juvenile salmonids (INPMEP, BPA#1999107300) , Fish Cr done in 2007 and 2008 ongoing annual sampling (ISMES)  Random snorkel surveys in Crooked Fork Creek (INPMEP). Page 27 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

 ISMES (BPA 199005500 ) $784K/yr  INPMEP (BPA 199107300) $785K/yr

Lochsa River Spatial Periodic  Adult redd distribution  In 2007 IDFG  No data on adult  Develop Distribution distribution B Run  Juvenile parr distribution adopted a rotating spawner alternative estimates with panel probabilistic distribution methods to ability to detect a GRTS design for  Inference of estimate spatial 15% change with assessing the spawner distribution (e.g., 80% certainty. abundance of distribution from fry surveys, radio juvenile parr is uncertain and acoustic salmonids tagging) (INPMEP, BPA#1999107300) , Fish Cr done in 2007 and 2008  Random snorkel surveys in Crooked Fork Creek (INPMEP).  ISMES (BPA 199005500 ) $784K/yr  INPMEP (BPA 199107300) $785K/yr Page 28 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Lochsa River Species  Short term  Age  Juvenile and adult   Genetic baseline 5-year rotating panel Diversity for baseline genetic B Run collection of  Sex ratios life history Representativenes needs to be phenotypes characteristics s of index streams maintained at samples (ISMES)  Size estimated at weir to entire  Long term regular intervals  Cohort structure and screw traps population collection of (i.e., scales,  Develop habitat genotypes  Run Timing lengths, PIT tags, and life history  DNA gender). model(s) to  There appear to synthesize be sufficient DNA available data to samples being extrapolate from collected to index samples to provide good baseline for future an appropriate ESA status review population scale. of genetic diversity. Since 2000, Idaho Steelhead Monitoring and Evaluation Studies (ISMES) has collected tissue samples from populations across all the various populations in the Clearwater and Salmon basins  In 2007 678 DNA samples were analyzed  ISMES (BPA 199005500 ) Page 29 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

$784K/yr 

Selway River Adults Annual population- Natural-origin Spawner Abundance  No steelhead  Data very limited . Need adult abundance RPA 50.5 IDFG BiOp Accord Abundance level estimates and age structure data proposes to increase B B Run weirs  It is expected that with a CV value on for index Run monitoring in  No hatchery fish GSI will accurately subpopulation average of 15% or Clearwater and Salmon released. identify this Investigate Genetic less. River drainages. To  Natural-origin population Parentage Analysis Techniques to Estimate meet RPA 50.5. BPA Snake River however this must Power analysis Spawner Abundance in contract 199005500 Steelhead MPG be verified. calculated for data ESA-listed Steelhead $150k/yr and population  No CV estimates Populations abundance via made (200732300) Genetic Stock Identification (GSI) at Lower Granite Dam began in 2008 $150K/yr (ISMES)

Selway River Adult Adult/Adult ratio  Sex ratio  IDFG Accord  Population is not  Need adult RPA 50.5 IDFG BiOp Accord 2 Productivity with low σ provides heavily influenced abundance and proposes to increase B B Run  Hatchery % RPA 50.7 $150,000/yr to do by hatchery age structure data Run monitoring in  Cohorts steelhead; GSI assessments for index Clearwater and Salmon  Harvest hatchery fraction River drainages. To (combined with data are lacking. subpopulation age and sex meet RPA 50.5. BPA  Estimates of  Develop surveys contract 199005500 comp.) in natural population of hatchery $150k/yr Clearwater and incidental spawner fraction Page 30 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Salmon River. mortality from in index streams  Annual parr recreational  Reevaluate fisheries are density juvenile sampling imprecise. monitoring design and verify  Estimating adult (surrogate for steelhead age structure adults) conducted abundance cannot assumptions by IDFG within be done needed for population BPA accurately at the productivity 199107300 population scale estimates using current   Develop habitat methods in high  Sport fishing for and turbid flows, and life cycle adult steelhead is juvenile estimates model(s) to not permitted are important as a synthesize within population proxy for adult available data to boundaries. productivity . extrapolate from  ISMES (BPA other populations. 199005500 ) $784K/yr

Selway River Juvenile Annual population-  Juvenile Migrant Abundance  NPT operates  Imprecision of  Increased PIT YES Explore feasibility of Productivity level estimates RPA 50.5 using GSI and age B Run  Smolt/Adult ratio screw trap in SARs at tagging or roll up with a CV value on Meadow Creek . population level SARs to larger comp. for smolts at average of 15% or LGR Steelhead not PIT-  Dispersed PIT scale less. tagged. tagging conducted  PIT-tag juvenile IDFG BiOp Accord  In 2007 IDFG in 1995-2006 steelhead at Power analysis proposes to increase B adopted a rotating (199107300) Meadow Creek calculated for Run monitoring in panel probabilistic  No CV estimates screw trap. data? Clearwater and Salmon GRTS design for made  Explore River drainages. To assessing the alternative meet RPA 50.5. BPA abundance of method of contract 199005500 juvenile estimating SARs $150k/yr Page 31 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

salmonids with precision (INPMEP, BPA#1999107300) , upper Selway done in 2008 other portions are planned for sampling as well  INPMEP (BPA 199107300) $785K/yr

Selway River Spatial Periodic  Adult redd distribution  In 2007 IDFG  No data on adult  Develop Distribution distribution B Run  Juvenile parr distribution adopted a rotating spawner alternative estimates with panel probabilistic distribution methods to ability to detect a GRTS design for  Inference of estimate spatial 15% change with assessing the spawner distribution (e.g., 80% certainty. abundance of distribution from fry surveys, radio juvenile parr is uncertain and acoustic salmonids upper tagging) Selway done in 2008 (INPMEP, BPA#1999107300) ,  INPMEP (BPA 199107300) $785K/yr Page 32 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

Selway River Species  Short term  Age  Limited life history   Genetic baseline 5-year rotating panel Diversity for baseline genetic B Run collection of  Sex ratios data. Representativenes needs to be phenotypes s of index streams maintained at samples (ISMES)  Size  Long term  There appear to to entire regular intervals  Cohort structure collection of be sufficient DNA population  Develop habitat samples being genotypes  Run Timing and life history collected to  DNA provide good model(s) to baseline for future synthesize ESA status review available data to of genetic extrapolate from diversity. Since index samples to 2000, Idaho an appropriate Steelhead Monitoring and population scale. Evaluation Studies (ISMES) has collected tissue samples from populations across all the various populations in the Clearwater and Salmon basins  In 2007 678 DNA samples were analyzed  DNA collected in upper Selway in 2008  ISMES (BPA 199005500 ) $784K/yr Page 33 SNAKE RIVER STEELHEAD DPS- CLEARWATER MPG- VSP MONITORING ANALYSIS FINAL VERSION 4/6/2009

MPG Data    Data have yet to be Review, summarize, synthesized at the and synthesize data by Analysis and population level population Support