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• 41. [Article] Willamette BiOp - Genetic Stock Identification and Relative Natural Production of Willamette River Steelhead

  Abstract -- We used genotypic data from 15 microsatellite loci to characterize the stock structure of Oncorhynchus mykiss in the upper Willamette River basin. We then used two analytical approaches, implemented ...

  Citation × Citation Citation Abstract Copy Title: Willamette BiOp - Genetic Stock Identification and Relative Natural Production of Willamette River Steelhead Abstract -- We used genotypic data from 15 microsatellite loci to characterize the stock structure of Oncorhynchus mykiss in the upper Willamette River basin. We then used two analytical approaches, implemented in the programs ONCOR and STRUCTURE, to assign (presumably) natural-origin, unmarked fish to their most likely reporting group or hybrid class. We investigated sibling relationships among unknown samples with the program ML RELATE. In the upper Willamette River, O. mykiss genetic structure can be characterized by four principal groups: summer steelhead of Skamania stock ancestry, eastern tributaries winter steelhead, western tributaries winter steelhead and resident rainbow trout. We found that about 10% of unmarked juvenile O. mykiss sampled at Willamette Falls in 2009-2011 were summer steelhead and that an additional 10% of samples were summer x winter steelhead hybrids. Most O. mykiss sampled from the McKenzie River were either summer steelhead or summer x winter steelhead hybrids. Natural production of pure summer steelhead appeared to be very low in the North and South Santiam rivers, though summer steelhead hybrids represented 11.1% and 14.8% of samples. Results from ML RELATE analyses appeared unreliable and inconclusive, and may have been limited by low genetic diversity among summer steelhead samples. We provide several recommendations to better understand and reduce potentially negative interactions between hatchery summer steelhead and native upper Willamette River O. mykiss populations. These include reductions in adult steelhead on natural spawning grounds, improved reproductive isolation between hatchery and native populations and additional research to evaluate genetic integrity within and among O. mykiss populations. Title: Willamette BiOp - Genetic Stock Identification and Relative Natural Production of Willamette River Steelhead Abstract -- We used genotypic data from 15 microsatellite loci to characterize the stock structure of Oncorhynchus mykiss in the upper Willamette River basin. We then used two analytical approaches, implemented in the programs ONCOR and STRUCTURE, to assign (presumably) natural-origin, unmarked fish to their most likely reporting group or hybrid class. We investigated sibling relationships among unknown samples with the program ML RELATE. In the upper Willamette River, O. mykiss genetic structure can be characterized by four principal groups: summer steelhead of Skamania stock ancestry, eastern tributaries winter steelhead, western tributaries winter steelhead and resident rainbow trout. We found that about 10% of unmarked juvenile O. mykiss sampled at Willamette Falls in 2009-2011 were summer steelhead and that an additional 10% of samples were summer x winter steelhead hybrids. Most O. mykiss sampled from the McKenzie River were either summer steelhead or summer x winter steelhead hybrids. Natural production of pure summer steelhead appeared to be very low in the North and South Santiam rivers, though summer steelhead hybrids represented 11.1% and 14.8% of samples. Results from ML RELATE analyses appeared unreliable and inconclusive, and may have been limited by low genetic diversity among summer steelhead samples. We provide several recommendations to better understand and reduce potentially negative interactions between hatchery summer steelhead and native upper Willamette River O. mykiss populations. These include reductions in adult steelhead on natural spawning grounds, improved reproductive isolation between hatchery and native populations and additional research to evaluate genetic integrity within and among O. mykiss populations. Close

• 42. [Article] Lower Snake River Compensation Plan; Oregon Evaluation Studies - 1995 and 1996 Annual Progress Report

  Abstract -- This report summarizes fish culture monitoring data for Lower Snake River Compensation Plan (LSRCP) facilities for each species. These data should serve as the basis for the analysis of trends ...

  Citation × Citation Citation Abstract Copy Title: Lower Snake River Compensation Plan; Oregon Evaluation Studies - 1995 and 1996 Annual Progress Report Abstract -- This report summarizes fish culture monitoring data for Lower Snake River Compensation Plan (LSRCP) facilities for each species. These data should serve as the basis for the analysis of trends in culture performance. Generally speaking, the data in this report were derived from hatchery inventories and standard databases (i.e., PSMFC, Coded-wire tag) or through standard measuring techniques. As such, specific protocols are usually not described. In cases where expansions of data or unique methodologies were used, protocols are described in more detail. Additional descriptions of protocols can be found in the 1995 and 1996 work statements (Carmichael 1995, 1996). Coded-wire tag (CWT) data that were collected from 1995-1996 adult returns is used to evaluate smolt-to-adult survival rates in experimental rearing and release groups. In 1995-1996, experimental treatments from which fish returned included acclimated vs. direct stream for steelhead and size-at-release for both steelhead and Chinook. In 1995-1996, experimental treatments for which fish were released included size-at-release, exercise, acclimation, and low density treatments for Chinook, acclimated vs. direct stream for both steelhead and Chinook, and forced vs. volitional release for steelhead. Analysis of specific survival studies will be completed once all brood years have returned and CWT data are complete for a given experiment. In addition, much of the data that we discuss in this report will be used in separate and specific evaluations of ongoing supplementation programs for both steelhead and Chinook in the Imnaha River basin. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Title: Lower Snake River Compensation Plan; Oregon Evaluation Studies - 1995 and 1996 Annual Progress Report Abstract -- This report summarizes fish culture monitoring data for Lower Snake River Compensation Plan (LSRCP) facilities for each species. These data should serve as the basis for the analysis of trends in culture performance. Generally speaking, the data in this report were derived from hatchery inventories and standard databases (i.e., PSMFC, Coded-wire tag) or through standard measuring techniques. As such, specific protocols are usually not described. In cases where expansions of data or unique methodologies were used, protocols are described in more detail. Additional descriptions of protocols can be found in the 1995 and 1996 work statements (Carmichael 1995, 1996). Coded-wire tag (CWT) data that were collected from 1995-1996 adult returns is used to evaluate smolt-to-adult survival rates in experimental rearing and release groups. In 1995-1996, experimental treatments from which fish returned included acclimated vs. direct stream for steelhead and size-at-release for both steelhead and Chinook. In 1995-1996, experimental treatments for which fish were released included size-at-release, exercise, acclimation, and low density treatments for Chinook, acclimated vs. direct stream for both steelhead and Chinook, and forced vs. volitional release for steelhead. Analysis of specific survival studies will be completed once all brood years have returned and CWT data are complete for a given experiment. In addition, much of the data that we discuss in this report will be used in separate and specific evaluations of ongoing supplementation programs for both steelhead and Chinook in the Imnaha River basin. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Close

• 43. [Article] Umatilla Basin Natural Production Monitoring and Evaluation; Annual Progress Report 1994 - 1995

  Abstract -- This report summarizes the activities of the Umatilla Basin Natural Production Monitoring and Evaluation Project (UBNPME) from September 30, 1994 to September 29, 1995. This program was funded ...

  Citation × Citation Citation Abstract Copy Title: Umatilla Basin Natural Production Monitoring and Evaluation; Annual Progress Report 1994 - 1995 Abstract -- This report summarizes the activities of the Umatilla Basin Natural Production Monitoring and Evaluation Project (UBNPME) from September 30, 1994 to September 29, 1995. This program was funded by Bonneville Power Administration and was managed under the Fisheries Program, Department of Natural Resources, Confederated Tribes of the Umatilla Indian Reservation. An estimated 36.7 km (22.6 miles) of stream habitat were inventoried on the Umatilla River, Moonshine, Mission, Cottonwood and Coonskin Creeks. A total of 384 of 3,652 (10.5%) habitat units were electrofished. The number of juvenile fish captured follows: 2,953 natural summer steelhead (including resident rainbow tout; Oncorhynchus mykiss), one hatchery steelhead, 341 natural chinook salmon (0. tshawytscha), 163 natural coho salmon (0. kisutch), five bull trout (Salvelinus confluentus), 185 mountain whitefish (Prosopium williamsoni), and six northern squawfish (Ptychocheilus oregonensis). The expanded population estimate for the areas surveyed was 73,716 salmonids with a mean density of 0.38 fish/m2. The following number of non-salmonids were visually estimated: 7,572 speckled dace (Rhinichthys osculus), 5,196 sculpin (Cottus spp.), 532 suckers (Catostomus spp.) and 191 redside shiners (Richardsonius balteatus). The gross estimated density of all non-salmonids combined was 0.84 fish/m2. The estimated ratio of non-salmonids to salmonids was 2.4: 1. Relative salmonid abundance, seasonal distribution and habitat utilization were monitored at index sites throughout the basin. During index site monitoring, the following species were collected in addition to those listed above: american shad (Alosa sapidissima), smallmouth bass (Micropterus dolomieu), carp (Cyprinus Carpio) and chiselmouth (Acrocheilus alutaceus). Thirty ­nine sites were electrofished during the spring and summer seasons, while 36 sites were sampled in the fall season. Index sites with the. highest mean salmonid catch/minute (fish/min.) during the three sample periods were located at the following sites: East Birch Creek (3.4 fish/min.), Boston Canyon Creek (3.2 fish/min.), Spring Creek (3.1 fish/min.) and upper Squaw Creek (3.0 fish/min.). The highest electrofishing catch rates were observed in the Umatilla River tributaries above river mile (RM) 70 in the August and September sample period (Table J-2 catalogs river miles with associated landmarks). During the November sample period, catch rates were highest in Birch Creek tributaries. Most salmonids were captured in slow water near the bank during the November and March sampling periods. A study of the migration movements and homing requirements of adult salmonids in the Umatilla River was conducted during the 1994-95 return years. Radio telemetry was used to evaluate the movements of adult salmonids past diversion dams in the lower Umatilla River and to determine migrational movements of salmonids following upstream transport. Radio transmitters were placed in 30 summer steelhead, 15 spring chinook, nine fall chinook, and eight coho salmon. Salmon were released at Three Mile Falls Dam (TMD). An additional 11 summer steelhead and ten spring chinook salmon were tagged, hauled upstream, and released at either Barnhart, Nolin, Thornhollow, or Imeques C-mem-ini-kem. On average, summer steelhead required 36 days to successfully migrate from TMD to Stanfield Dam. Spring chinook required 18 days. Average passage times for summer steelhead (hours and minutes) at Westland, Feed Canal, and Stanfield Dams were 13:06, 83:24, and 2:58, respectively. Spring chinook salmon required 04:30 at Westland, 89:42 at Feed Canal, and 04:01 at Stanfield Dams. Migrational delays were observed at Feed Canal Dam at flows ranging from 563 to 1,601 cubic feet/second (cfs). Thirty-eight percent of the fish ladder at Westland Dam, 75% at Feed canal, and 31% at Stanfield Dam. Average passage times at Feed Canal Dam (1995) were more than 15 times those at Stanfield Dam in 1994 and more than 20 times those at Stanfield Dam in 1995. Data related to homing and passage needs of Umatilla River salmonids was investigated in an attempt to maximize homing to the Umatilla River. Straying rates of adult summer steelhead and spring chinook salmon were found to be low while coho and fall chinook salmon stray rates were high in some groups, particularly adult returns from subyearling smolt releases of fall chinook salmon. Attraction flows of from the mouth of the Umatilla River of at least 150 cfs were required to encourage migration and reduce straying of fall chinook and coho salmon. Significant numbers of summer steelhead entered when flows exceeded 500 cfs. Spring chinook salmon entry was variable with fish entering at flows ranging from 150 to more than 2,000 cfs. Adult anadromous salmonids potentially available to spawn above TMD from August 26, 1994 to June 27, 1995 included: 593 adult and 530 jack fall chinook salmon (1994 brood), 879 adult and 54 jack coho salmon (1994 brood), 784 natural and 509 hatchery summer steelhead (1995 brood), and 378 adult and 62 jack spring chinook salmon (1995 brood). During escapement surveys (fall of 1994), a total of 82 fall chinook salmon redds, 24 coho salmon redds and seven unidentified salmon redds (112 redds total, 2.6/mile) were enumerated along 42.3 miles of the mainstem above TMD. In 1995, we enumerated and flagged 126 summer steelhead redds (3.6 redds/mile) along 35.3 miles of lateral tributaries of the Umatilla River. Also enumerated were 90 spring chinook salmon redds (1.6 redds/mile) along 55.8 miles of the mainstem. Ninety-six percent of the adult fall chinook salmon carcasses examined had spawned while 94% of the coho had spawned; 66.8 % of the spring chinook salmon carcasses examined bad spawned. A total of 49.3% of spring chinook salmon released above TMD were sampled during spawning ground surveys and 60 coded wire tags (CWTs) were recovered from 78 adipose clipped fish. The rotary screw trap in the Umatilla River (RM 76) operated 63 of 113 days from September 21, 1994 to January 13, 1995. The trap captured 596 juvenile steelhead with a mean trap efficiency rate of 9.9%. A total of 1,368 juvenile chinook salmon were captured with a mean trap efficiency rate of 28. 8 % . The rotary screw trap at the Imeques C-mem-ini-kem site (RM 79.5) operated 43 out of 43 days from May 5 through June 16, 1995. The trap captured 304 natural juvenile steelhead with a mean trap efficiency rate of 6.6%. A total of 102 natural juvenile chinook salmon were captured with a mean trap efficiency rate of 10.5%. The rotary screw trap at the Barnhart site (RM 42,2) operated 87 out of 125 days from March 3 to June I, 1995. The trap captured 105 natural juvenile steelhead, 247 natural juvenile chinook salmon, five natural coho salmon, 6,265 hatchery juvenile chinook salmon, 467 hatchery steelhead and 16,844 hatchery coho salmon. Mean trap efficiency rates ranged from 2.3 to 5.7% . Harvest monitors estimated that tribal anglers harvested 25 hatchery and five natural summer steelhead during the spring of 1995. There was no spring chinook salmon fishery in the Umatilla River during 1995 because of the low number of returning adults. Scale analysis determined that over 85 .0% of naturally produced juvenile summer steelhead sampled during biological and index surveys were age O+ or l +. Naturally produced summer steelhead adults, returning to the Umatilla River in 1994-95, were mostly from the 1990 (46.4%) and 1991 (33.9%) brood years. Title: Umatilla Basin Natural Production Monitoring and Evaluation; Annual Progress Report 1994 - 1995 Abstract -- This report summarizes the activities of the Umatilla Basin Natural Production Monitoring and Evaluation Project (UBNPME) from September 30, 1994 to September 29, 1995. This program was funded by Bonneville Power Administration and was managed under the Fisheries Program, Department of Natural Resources, Confederated Tribes of the Umatilla Indian Reservation. An estimated 36.7 km (22.6 miles) of stream habitat were inventoried on the Umatilla River, Moonshine, Mission, Cottonwood and Coonskin Creeks. A total of 384 of 3,652 (10.5%) habitat units were electrofished. The number of juvenile fish captured follows: 2,953 natural summer steelhead (including resident rainbow tout; Oncorhynchus mykiss), one hatchery steelhead, 341 natural chinook salmon (0. tshawytscha), 163 natural coho salmon (0. kisutch), five bull trout (Salvelinus confluentus), 185 mountain whitefish (Prosopium williamsoni), and six northern squawfish (Ptychocheilus oregonensis). The expanded population estimate for the areas surveyed was 73,716 salmonids with a mean density of 0.38 fish/m2. The following number of non-salmonids were visually estimated: 7,572 speckled dace (Rhinichthys osculus), 5,196 sculpin (Cottus spp.), 532 suckers (Catostomus spp.) and 191 redside shiners (Richardsonius balteatus). The gross estimated density of all non-salmonids combined was 0.84 fish/m2. The estimated ratio of non-salmonids to salmonids was 2.4: 1. Relative salmonid abundance, seasonal distribution and habitat utilization were monitored at index sites throughout the basin. During index site monitoring, the following species were collected in addition to those listed above: american shad (Alosa sapidissima), smallmouth bass (Micropterus dolomieu), carp (Cyprinus Carpio) and chiselmouth (Acrocheilus alutaceus). Thirty ­nine sites were electrofished during the spring and summer seasons, while 36 sites were sampled in the fall season. Index sites with the. highest mean salmonid catch/minute (fish/min.) during the three sample periods were located at the following sites: East Birch Creek (3.4 fish/min.), Boston Canyon Creek (3.2 fish/min.), Spring Creek (3.1 fish/min.) and upper Squaw Creek (3.0 fish/min.). The highest electrofishing catch rates were observed in the Umatilla River tributaries above river mile (RM) 70 in the August and September sample period (Table J-2 catalogs river miles with associated landmarks). During the November sample period, catch rates were highest in Birch Creek tributaries. Most salmonids were captured in slow water near the bank during the November and March sampling periods. A study of the migration movements and homing requirements of adult salmonids in the Umatilla River was conducted during the 1994-95 return years. Radio telemetry was used to evaluate the movements of adult salmonids past diversion dams in the lower Umatilla River and to determine migrational movements of salmonids following upstream transport. Radio transmitters were placed in 30 summer steelhead, 15 spring chinook, nine fall chinook, and eight coho salmon. Salmon were released at Three Mile Falls Dam (TMD). An additional 11 summer steelhead and ten spring chinook salmon were tagged, hauled upstream, and released at either Barnhart, Nolin, Thornhollow, or Imeques C-mem-ini-kem. On average, summer steelhead required 36 days to successfully migrate from TMD to Stanfield Dam. Spring chinook required 18 days. Average passage times for summer steelhead (hours and minutes) at Westland, Feed Canal, and Stanfield Dams were 13:06, 83:24, and 2:58, respectively. Spring chinook salmon required 04:30 at Westland, 89:42 at Feed Canal, and 04:01 at Stanfield Dams. Migrational delays were observed at Feed Canal Dam at flows ranging from 563 to 1,601 cubic feet/second (cfs). Thirty-eight percent of the fish ladder at Westland Dam, 75% at Feed canal, and 31% at Stanfield Dam. Average passage times at Feed Canal Dam (1995) were more than 15 times those at Stanfield Dam in 1994 and more than 20 times those at Stanfield Dam in 1995. Data related to homing and passage needs of Umatilla River salmonids was investigated in an attempt to maximize homing to the Umatilla River. Straying rates of adult summer steelhead and spring chinook salmon were found to be low while coho and fall chinook salmon stray rates were high in some groups, particularly adult returns from subyearling smolt releases of fall chinook salmon. Attraction flows of from the mouth of the Umatilla River of at least 150 cfs were required to encourage migration and reduce straying of fall chinook and coho salmon. Significant numbers of summer steelhead entered when flows exceeded 500 cfs. Spring chinook salmon entry was variable with fish entering at flows ranging from 150 to more than 2,000 cfs. Adult anadromous salmonids potentially available to spawn above TMD from August 26, 1994 to June 27, 1995 included: 593 adult and 530 jack fall chinook salmon (1994 brood), 879 adult and 54 jack coho salmon (1994 brood), 784 natural and 509 hatchery summer steelhead (1995 brood), and 378 adult and 62 jack spring chinook salmon (1995 brood). During escapement surveys (fall of 1994), a total of 82 fall chinook salmon redds, 24 coho salmon redds and seven unidentified salmon redds (112 redds total, 2.6/mile) were enumerated along 42.3 miles of the mainstem above TMD. In 1995, we enumerated and flagged 126 summer steelhead redds (3.6 redds/mile) along 35.3 miles of lateral tributaries of the Umatilla River. Also enumerated were 90 spring chinook salmon redds (1.6 redds/mile) along 55.8 miles of the mainstem. Ninety-six percent of the adult fall chinook salmon carcasses examined had spawned while 94% of the coho had spawned; 66.8 % of the spring chinook salmon carcasses examined bad spawned. A total of 49.3% of spring chinook salmon released above TMD were sampled during spawning ground surveys and 60 coded wire tags (CWTs) were recovered from 78 adipose clipped fish. The rotary screw trap in the Umatilla River (RM 76) operated 63 of 113 days from September 21, 1994 to January 13, 1995. The trap captured 596 juvenile steelhead with a mean trap efficiency rate of 9.9%. A total of 1,368 juvenile chinook salmon were captured with a mean trap efficiency rate of 28. 8 % . The rotary screw trap at the Imeques C-mem-ini-kem site (RM 79.5) operated 43 out of 43 days from May 5 through June 16, 1995. The trap captured 304 natural juvenile steelhead with a mean trap efficiency rate of 6.6%. A total of 102 natural juvenile chinook salmon were captured with a mean trap efficiency rate of 10.5%. The rotary screw trap at the Barnhart site (RM 42,2) operated 87 out of 125 days from March 3 to June I, 1995. The trap captured 105 natural juvenile steelhead, 247 natural juvenile chinook salmon, five natural coho salmon, 6,265 hatchery juvenile chinook salmon, 467 hatchery steelhead and 16,844 hatchery coho salmon. Mean trap efficiency rates ranged from 2.3 to 5.7% . Harvest monitors estimated that tribal anglers harvested 25 hatchery and five natural summer steelhead during the spring of 1995. There was no spring chinook salmon fishery in the Umatilla River during 1995 because of the low number of returning adults. Scale analysis determined that over 85 .0% of naturally produced juvenile summer steelhead sampled during biological and index surveys were age O+ or l +. Naturally produced summer steelhead adults, returning to the Umatilla River in 1994-95, were mostly from the 1990 (46.4%) and 1991 (33.9%) brood years. Close