RefiningourunderstandingofearlyandlatemigrationofadultUpperColumbiaspringandSnakeRiverspring/summerChinooksalmon:passagetiming,traveltime,fallbackandsurvival Lisa Crozier, Elene Dorfmeier, Tiffani Marsh, Ben Sandford, Dan Widener Report of research by Fish Ecology Division, Northwest Fisheries Science Center National Marine Fisheries Service 2725 Montlake Blvd. East Seattle, WA 98112 March 2016

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ExecutiveSummary Adult spring/summer Chinook salmon migrate through the lower Columbia River over a protracted period from March through September. We explored run timing, travel time, survival, and fallback for groups of Chinook salmon from two evolutionarily significant units (ESUs) listed under the U.S. Endangered Species Act. Passage metrics were evaluated for 5,062 adults from the Upper Columbia spring run Chinook salmon ESU and 11,496 from the Snake River spring/summer run Chinook salmon ESU. All analyses were based on detections fish marked as juveniles with passive integrated transponder (PIT) tags. Although the numbers of tagged fish are not necessarily representative of all levels of biological aggregation, we included fish from all of the major population groups (MPGs) of both ESUs, and many individual populations within these MPGs, as determined by release site in the PIT Tag Information System (PTAGIS) database. Among fish from these ESUs, the earliest migrants were mostly from the Upper Columbia ESU, although fish originating in the Lower Snake River were also among the earliest to arrive at Bonneville Dam. Fish from the Clearwater and Rapid River were much earlier than any other Snake River populations. For analyses of run timing and its effects on survival and travel time within the hydrosystem, we separated the Snake River spring/summer run ESU into early and late groups. Most fish from the Lower Snake, Grande Ronde, Middle Fork Salmon, and Upper Salmon River MPGs fell into the early group. However, Pahsimeroi and Imnaha fish were separated from their respective MPGs (Upper Salmon River and Grande Ronde) because these fish appeared to have distinctly later run timing. They were grouped as late migrants, along with fish from the South Fork Salmon River MPG. Variation in run timing within and among tagged groups was extensive, even within early and late population groupings; therefore, further understanding of the factors that determine run timing is still needed. Nonetheless, median run timing of fish from the South Fork Salmon River MPG, along with those fish from the Imnaha and Pahsimeroi Rivers, was 2-4 weeks later than that of other Snake River spring/summer Chinook. Consequently, 30-40% of these late fish passed McNary Dam after 15 June, when the summer harvest period begins. In late-arrival years (2006, 2008, and 2011), a majority of the tagged fish from these late-migrant groups migrated during the summer harvest period.

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Hatchery fish from the upper Columbia showed a strong tendency to arrive at Bonneville Dam before wild fish. Hatchery fish from the Wenatchee Basin, in particular, entered the reach from Bonneville to McNary Dam 3 weeks earlier, on average, than wild fish—a difference of 1.5 standard deviations. For Snake River hatchery fish, arrival timing at Bonneville was more similar to that of wild fish, or in some cases later. Variation in survival across years was greater among the three late-migrant Snake River tag groups than among the earlier groups. Snake River late-migrant groups exhibited especially low survival in the reach from Bonneville to McNary Dam in 2011, 2014 and 2015 (range 61-67%). Within this same reach, and during the same years, late Snake River migrants also displayed unusually long median travel times (8 d). Otherwise, median travel time was 5-6.5 d through this stretch across all groups. Two factors stood out as affecting survival within populations. 1) Estimated survival during the upstream migration was higher for wild than for

hatchery fish from both Chinook salmon ESUs (0.84 vs. 0.81 for Upper Columbia and 0.84 vs. 0.79 for Snake River fish).

2) For Snake River fish, estimated survival over the upstream migration was higher for fish that had migrated downstream naturally as juveniles than for fish that had been transported downstream in barges (0.81 vs 0.79).

After controlling for early vs. late runs, hatchery vs. natural origin, and juvenile migration history of transport vs. inriver migration, there was no difference survival from Bonneville to McNary Dam between Snake and Upper Columbia River fish.

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Contents Executive Summary ........................................................................................................... iii  Introduction ......................................................................................................................... 1  Study Fish and Groups for Comparison .............................................................................. 5 

Methods................................................................................................................... 5 Results ................................................................................................................... 10 

Adult Run Timing and Migration Rate ............................................................................. 14 

Methods................................................................................................................. 14 Results ................................................................................................................... 14 

Summary statistics .................................................................................... 17 Comparisons by rearing type and origin ................................................... 20 Migration rate ............................................................................................ 21 Effects of timing on harvest exposure ...................................................... 25 

Adult Migration Survival .................................................................................................. 28 

Methods................................................................................................................. 28 Study groups and reach for comparison .................................................... 29 Juvenile transport groups .......................................................................... 29 

Results ................................................................................................................... 31 Comparisons by origin and juvenile migration history ............................. 31 Survival from Bonneville to McNary Dam for Snake River Fish ............ 35 Survival from Bonneville to Rock Island Dam for Columbia River Fish 39 

Fallback and Reascension ................................................................................................. 42 

Methods................................................................................................................. 42 Results ................................................................................................................... 43 

Snake River Spring/Summer Run Chinook Salmon ................................. 43 Upper Columbia River Spring Run Chinook Salmon............................... 47 

Conclusions ....................................................................................................................... 50  References ......................................................................................................................... 52 

Introduction The Columbia River Basin supports some of the most productive salmon runs in the world. Millions of wild and hatchery Chinook salmon migrate through the mainstem Columbia and Snake Rivers every year. An estimated 54 biologically distinct populations of spring, summer, and fall-run Chinook salmon still migrate to mid and upper reaches within the basin. However, 78 populations in this region are thought to have gone extinct (Gustafson et al. 2007). Remaining populations of spring and spring-summer Chinook salmon have been grouped into evolutionarily significant units (ESU) for the purpose of listing status under the U.S. Endangered Species Act. Among these ESUs, the Upper Columbia spring run Chinook salmon ESU is now listed as endangered, while the Snake River spring/summer-run Chinook salmon ESU is listed as threatened. Fish from both ESUs migrate through various fisheries, which target hatchery fish and attempt to minimize impact on listed species. They also swim past a system of major hydroelectric dams. Harvest and hydrosystem managers are responsible for minimizing negative impacts on listed fish. Factors that affect adult survival include inherent characteristics of the fish prior to entering the Columbia River, such as rearing history, origin, and juvenile migration history, as well as conditions encountered en route (Crozier et al. 2014). In the 1960s, transportation of juvenile fish was implemented to increase juvenile survival and adult returns of Snake River salmonids. However, transportation has also been shown to impair homing ability and increase rates of straying into non-natal rivers (Keefer et al. 2008). These traits may be associated with increased adult mortality. Conditions that affect survival en route are strongly influenced by the timing of adult migration due to seasonal patterns in temperature and flow, as well as anthropogenic factors such as harvest openings, catch limits, and spill at dams. Migration timing is one of the most locally adapted traits in salmon (Crozier and Hutchings 2014) and varies naturally among the populations studied here. Juvenile management also varies among populations and across years. Therefore, when studying the influence of various factors on adult survival, it is important to identify individual populations as much as possible. We identified fish to ESU, major population group (MPG), and individual population based on juvenile tagging records. To help identify the causes of mortality in adult migrants, we analyzed migration timing and reach survival of spring and spring/summer Chinook salmon from 2004 to

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2015. Our analysis was based on fish tagged with passive integrated transponders (PIT) as juveniles. We used release site to infer population and included only release sites within a single major population group (MPG) or natal stream (based on definitions in Ford 2011). We focused on wild fish as much as possible, comparing them to hatchery fish in cases where behavior was relatively similar. Even so, there may be multiple biological populations might be associated with a single release site. We acknowledge that tagging was conducted for other purposes, and is not proportionally representative of all biological populations within these ESUs. We therefore refer to these population groups as “tag groups” or use the term “population” loosely. Our analysis examined the migration timing and survival of 5,062 fish from the upper Columbia River spring run ESU and 11,496 fish from the Snake River spring/summer run ESU. Fish from the upper Columbia ESU included all three extant natural populations (Wenatchee, Entiat and Methow). Fish from the Snake ESU included all major listed population groups listed in the ESU (Grande Ronde, Lower Snake, Middle Fork Salmon, South Fork Salmon, and Upper Salmon). We describe some characteristics of additional fish from the Clearwater River and Rapid River Hatchery because they represent major elements of the spring Chinook run at large, but our survival analyses focused on threatened and endangered fish. To the extent possible, we followed established terminology to describe comparisons within biological levels of aggregation. However, we found the terms population, major population group, and ESU were not sufficient to classify groups of fish for our analysis. Similarly, the terms spring and summer have been used within the Snake River ESU in various ways that were not necessarily consistent with our findings. For this report, therefore, we applied the terms early and late instead of spring and summer, based on exploration of return timing by release site. We split particular tag groups that showed distinct run timing compared to the rest of the MPG. We hope this process will help to refine our understanding of run timing within each group. We use the term run to compare three groups: a) all upper Columbia spring Chinook, b) Snake River early run and c) Snake River late-run groups. The term tag group refers to populations of the upper Columbia River ESU, but to a mix of MPGs and populations in the Snake River ESU. We define early and late Snake River groups on the basis of observed run timing.

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In this analysis, we sought to characterize run-timing and survival by 1) tag group (MPG or population when we had sufficient data) and 2) run timing (upper Columbia, early Snake and late Snake), 3) hatchery vs. wild origin, and 4) juvenile transportation history. Fisheries have different quotas before and after 15 June, so we also summarize the percent of each tag group within the Zone 6 fishery management area (between Bonneville and McNary Dams) in relation to this reference date. We also summarize characteristics of travel time between dams and fallback over dams for fish that migrated between 2004 and 2014. Fallback (Boggs et al. 2004) has been linked to survival and a history of juvenile transportation (Crozier et al. 2014). Information about fallback and reacension rates in Chinook salmon could be used to investigate differences in adult salmonid migration behavior based on juvenile migration history characteristics and to further analyze the effects of fallback on passage survival through the hydrosystem.

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StudyFishandGroupsforComparison

Methods We compared adult migration timing and survival among listed stocks of upper Columbia River spring run and Snake River spring/summer run Chinook salmon over the 12-year period from 2004 to 2015. We constructed individual passage histories based on PIT-tag detections from instream monitoring systems in tributaries and from each dam along the respective Columbia and Snake River migration routes. To develop individual recapture and migration histories, we queried the PIT Tag Information System database (PTAGIS 2015) for juvenile tag files from years 2001-2015 and interrogation files from 2004-2015. These queries included only spring, summer, and unknown runs of hatchery and wild Chinook salmon. Thus, study fish were comprised of fish with PTAGIS species code 1, run codes 1, 2, or 5, and rear codes H and W. To avoid using fish tagged as adults (which cannot be ascribed to population), we excluded fish with a length at tagging of >300 mm. However, we included fish that were missing fork lengths but met the other criteria. Fish that matured after one year or less in the ocean (jacks) were excluded by selecting only fish that had returned at least 2 years after the juvenile migration year. Fish were initially grouped by ESU and major population group (MPG) based on juvenile release site data from PTAGIS (Tables 1 and 2). We used the river kilometer (rkm) code of each release site to identify fish that originated from the Snake (beginning with 522) or Upper Columbia Basin (beginning with ≥ 639). If the release site was located within the boundary of a single population (Ford 2011), it was further identified as belonging to that population. Fish with tagging or release sites at major dams were excluded because the geographic origins of these fish could not be determined from tagging records (Table 3). Separate analyses were conducted for individual populations consisting of 200 fish or more; populations with fewer than 200 fish were grouped within their respective MPGs.

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Table 1. Names of fish release sites in the PTAGIS database used to determine groups within the Upper Columbia River spring run Chinook salmon ESU. This ESU has only one MPG—the Upper Columbia River spring run Chinook salmon MPG. Therefore, fish were grouped for analysis at the population level.

Study fish from the Upper Columbia River spring run ESU by PTAGIS release site

Entiat River population Wenatchee River population Entiat River Wenatchee River Chelan River Chiwawa River Entiat National Fish Hatchery Nason Creek Entiat NFH Peshastin River Mad River (Entiat River watershed) Upper Wenatchee Nason Creek (tributary to Wenatchee River) Methow River population West Monitor Bridge Methow River Upper Wenatchee trap Methow Smolt Trap at McFarland White River Creek Road Bridge White River, Wenatchee River Basin Biddle Acclimation Pond Chiwawa Rearing Ponda Chewuch Acclimation Pond Chiwawa River Trapb Chewuch Acclimation Pond (WDFW) Leavenworth National Fish Hatchery or Mid-Valley Acclimation Pond, Leavenworth NFH Methow River Watershed Upper Wenatchee Methow Hatchery Lake Wenatchee Twisp Acclimation Pond Wenatchee River trap at West Monitor Bridge Wolf Creek Upper Wenatchee smolt trap just below Lake Wolf Creek, Methow River Wenatchee

Biddle Acclimation Pond on Wolf Creek, Methow River Basin

Rearing Pond in the back channel to Winthrop National Fish Hatchery Twisp Acclimation Pond (WDFW) Winthrop National Fish Hatchery Winthrop NFH Chewuch River Twisp River

a Located 4 km above Chiwawa River b Located 0.5 km below CHIP acclimation pond

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Table 2. Names of fish release sites in the PTAGIS database used to determine groups from the Snake River ESU. Groups within the Grande Ronde (Imnaha) and Upper Salmon (Pahsimeroi) MPGs were evaluated separately because of differences in run timing between these populations and their respective MPGs.

Snake River release sites in the PTAGIS database by major population group (MPG) or tag group Grand Ronde MPG South Fork Salmon River MPG Catherine Creek Secesh River Grande Ronde River Secesh River Screw Trap Lookingglass Creek Summit Creek, Secesh River Basin Lostine River Johnson Creek Minam River Johnson Creek Trap Catherine Creek Pond Knox Bridge Grande Ronde River Lake Creek Grande Ronde River Pond Little Salmon River Grande Ronde River Trap South Fork Salmon River Grande Ronde to Wallowa River* South Fork Salmon River Trap Lostine River Lower SFSR Trap at rkm 61 Lookingglass Hatchery Lostine River Pond Upper Salmon River MPG Lookingglass Creek Hayden Creek Hayden Creek, Lemhi River Basin Imnaha River (Grande Ronde MPG) Herd Creek Imnaha Trap Lemhi River Imnaha River Weir Lemhi River Weir Imnaha River Big Springs Creek, Lemhi River Basin Sawtooth Trap Lower Snake River MPG West Fork Yankee Fork Salmon River Tucannon River East Fork Salmon River Curl Lake Rearing Pond Sawtooth Trap Valley Creek Middle Fork Salmon River MPG Yankee Fork Salmon River Capehorn Creek Sawtooth Hatchery Bear Valley Creek Big Creek Camas Creek Pahsimeroi River (Upper Salmon MPG) Chamberlain Creek Pahsimeroi Pond Elk Creek Pahsimeroi River Trap Loon Creek Pahsimeroi River Marsh Creek Trap Marsh Creek Lower Marsh Creek Trap at rkm 8 Sulphur Creek West Fork Chamberlain Creek

* To headwaters (km 131-325)

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Table 3. Names of release sites in PTAGIS that were excluded from analyses.

Release sites excluded from tag files Columbia River Mainstem McNary Dam Priest Rapids Dam Rock Island Dam Rocky Reach Dam Wells Dam

Snake River Basin Ice Harbor Dam Lower Monumental Dam Little Goose Dam Lower Granite Dam South Fork Salmon River

Yakima River Basin Prosser Dam Prosser Kelt Facility

Our primary intent was to characterize timing and survival of fish within the Upper Columbia spring run or Snake River spring/summer run Chinook salmon ESUs. We excluded fish from the Clearwater (522.244) and Rapid River (522.303.140.007). Fish from these two basins return relatively early compared to other fish from the Snake River ESU (Figure 1). Therefore, they were excluded from evaluations of run time. Spring Chinook salmon originating in the Clearwater River returned as adults earlier than other spring/summer Chinook populations in the Snake River ESU. Fish from Rapid River Hatchery were considered part of the South Fork Salmon MPG because the hatchery lies within the Little Salmon River. However, Rapid River Hatchery produces early run fish, while most other fish from the South Fork Salmon River are late-run.

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Figure 1. Cumulative distribution of adult spring and spring/summer Chinook salmon

arriving at Bonneville (left panel), and McNary Dam (right panel), 2004-2015. Populations designated Snake early are from the Lower Snake, Middle Fork Salmon, Upper Salmon excluding Pahsimeroi, and Grande Ronde excluding Imnaha. Populations designated Snake late are from the South Fork Salmon, Pahsimeroi, and Imnaha Rivers.

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Results All years combined, a total of 5,062 fish from upper Columbia and 11,496 fish from Snake River met the criteria for at least one of our tag groups (Table 4). Returns of PIT-tagged adults were most abundant in 2004 and 2010-2015. Among adult returns of tagged fish from the Upper Columbia ESU, a majority were from the Wenatchee River (67%), with 20% from the Methow, and 13% from the Entiat River (Tables 4 and 5). Most of these fish (83%) were of hatchery origin. Since 2007, adult returns from the Entiat River population have been wild fish, reflecting cessation of hatchery activities in that drainage. Among adult returns of tagged fish from the Snake River ESU over all years combined, a majority were from the South Fork Salmon or Grande Ronde River MPGs (41% each, Table 5). Remaining adults were from the Upper Salmon (11%), Middle Fork Salmon (4.5%), or Lower Snake MPGs (2.5%). Fish from the Imnaha River comprised 48% of the tagged adult returns from the Grande Ronde MPG, and fish from the Pahsimeroi River comprised 30% of returning tagged adults from the Upper Salmon River MPG. Tagged adults returning from the Middle Fork Salmon River MPG were exclusively wild fish; however, among tagged adults from the Snake River ESU overall, most were hatchery fish (66%).

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Table 4. Numbers by tag group of PIT-tagged spring/summer Chinook detected at Bonneville Dam as adults by return year.

Major population group (MPG) or sub-group 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015

Total (n) (%)

Snake River spring/summer run Chinook salmon ESU Grande Ronde 4,754 41 Grande Ronde early 192 92 69 50 162 159 478 416 261 100 233 266 2,478 22 Imnaha late 166 122 89 60 129 175 478 403 222 86 124 222 2,276 48 Lower Snake early 2 3 0 0 2 12 61 37 44 47 29 57 294 3 Middle Fork Salmon early 15 7 0 1 3 13 140 120 64 46 56 54 519 5 South Fork Salmon late 525 286 188 231 488 408 627 397 332 225 373 591 4,671 41 Upper Salmon 1,258 11 Upper Salmon spr early 22 11 13 14 32 95 125 91 95 68 119 197 882 70 Pahsimeroi late 4 1 5 3 5 9 103 109 17 12 50 58 376 30

Snake River total 926 522 364 359 821 871 2,012 1,573 1,035 584 984 1,445 11,496

Upper Columbia River spring run Chinook salmon ESU Entiat 117 132 140 26 11 4 70 58 49 21 22 35 685 13 Methow 81 83 118 6 12 14 57 29 158 76 195 232 1,061 20 Wenatchee 614 598 394 63 91 110 330 240 271 160 172 273 3,316 67

Upper Columbia R total 812 813 652 95 114 128 457 327 478 257 389 540 5,062

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Table 5. Proportions of fish from tag groups detected at Bonneville Dam adult returns by year.

Major population group (MPG) or sub-group

Proportions of yearling Chinook detected at Bonneville Dam 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015

Snake River spring/summer run Chinook salmon ESU

Grande Ronde Early 0.21 0.18 0.19 0.14 0.20 0.18 0.24 0.26 0.25 0.17 0.24 0.18

Imnaha Late 0.18 0.23 0.24 0.17 0.16 0.20 0.24 0.26 0.21 0.15 0.13 0.15

Lower Snake Early 0.00 0.01 0.00 0.00 0.00 0.01 0.03 0.02 0.04 0.08 0.03 0.04

Middle Fork Salmon Early 0.02 0.01 0.00 0.00 0.00 0.01 0.07 0.08 0.06 0.08 0.06 0.04

Pahsimeroi Late 0.00 0.00 0.01 0.01 0.01 0.01 0.05 0.07 0.02 0.02 0.05 0.04

South Fork Salmon Late 0.57 0.55 0.52 0.64 0.59 0.47 0.31 0.25 0.32 0.39 0.38 0.41

Upper Salmon spring Early 0.02 0.02 0.04 0.04 0.04 0.11 0.06 0.06 0.09 0.12 0.12 0.14

Upper Columbia River spring run Chinook salmon ESU

Entiat 0.14 0.16 0.21 0.27 0.10 0.03 0.15 0.18 0.10 0.08 0.06 0.06

Methow 0.10 0.10 0.18 0.06 0.11 0.11 0.12 0.09 0.33 0.30 0.50 0.43

Wenatchee 0.76 0.74 0.60 0.66 0.80 0.86 0.72 0.73 0.57 0.62 0.44 0.51

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Table 6. Numbers of hatchery vs. wild spring/summer Chinook comprising totals shown in Table 4.

Major population group (MPG) or sub-group

2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015Snake River spring/summer run Chinook salmon ESU

Hatchery Grande Ronde 149 70 43 31 107 89 343 255 178 48 128 151Imnaha 116 92 51 36 112 130 309 226 131 58 55 167Lower Snake 1 1 0 0 1 2 30 9 37 32 12 25South Fork Salmon 477 275 174 219 428 334 444 263 208 141 288 541Upper Salmon spring 2 0 0 0 4 56 54 25 52 21 41 97Pahsimeroi 3 1 1 0 0 2 89 100 12 2 32 38

Hatchery total 748 439 269 286 652 613 1,269 878 618 302 556 1,019

Wild Grande Ronde 43 22 26 19 55 70 135 161 83 52 105 115Imnaha 50 30 38 24 17 45 169 177 91 28 69 55Lower Snake 1 2 0 0 1 10 31 28 7 15 17 32Middle Fork Salmon 15 7 0 1 3 13 140 120 64 46 56 54South Fork Salmon 48 11 14 12 60 74 183 134 124 84 85 50Upper Salmon spring 20 11 13 14 28 39 71 66 43 47 78 100Pahsimeroi 1 0 4 3 5 7 14 9 5 10 18 20

Wild total 178 83 95 73 169 258 743 695 417 282 428 426 Upper Columbia River spring run Chinook salmon ESUHatchery Entiat 117 130 136 21 6 1 0 1 0 0 0 0Methow 81 83 118 5 9 9 30 6 152 69 184 213Wenatchee 614 593 392 62 68 81 232 119 193 129 129 222

Hatchery total 812 806 646 88 83 91 262 126 345 198 313 435

Wild Entiat 0 2 4 5 5 3 70 57 49 21 22 35Methow 0 0 0 1 3 5 27 23 6 7 11 19Wenatchee 0 5 2 1 23 29 98 121 78 31 43 51

Wild Total 0 7 6 7 31 37 195 201 133 59 76 105

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AdultRunTimingandMigrationRate

Methods Arrival day was defined as the date of first detection at each dam. Travel time was calculated as the number of days from last detection at one dam to first detection at the next site upstream. We calculated descriptive migration timing statistics for each tag group, specifically: the 5, 25, 50, 75, and 95th quantiles of the date each group was detected at Bonneville and McNary Dams. We summarized individual years and the 11-year average.

Results All three upper Columbia River populations arrived at Bonneville Dam relatively early (Figure 2 Wenatchee, Entiat, and Methow; Table 7). The Lower Snake River MPG was also very early. Most MPGs in the Snake River spring/summer run Chinook salmon ESU are considered spring-run dominated with the exception the South Fork Salmon River MPG. However, within each MPG, certain populations had later return timing. Visual inspection of our data indicated that for groups within the Upper Salmon and Grande Ronde MPGs, run timing was highly bimodal. Further data exploration revealed that each of these MPGs included a population with substantially later run timing than the remaining fish. Imnaha fish were then separated from other Grande Ronde populations, and Pahsimeroi fish were separated from other Upper Salmon populations. Both had relatively large numbers of fish at least in some years, and distinctly later run timing compared with the MPG as a whole. This adjustment did not remove all of the bimodality, which can still be seen for Pahsimeroi fish in Figure 2. Exploration of adult run timing by release-site group showed a more protracted gradation of median return times (Figure 3). Tagged fish released from some sites still spanned a wide range of adult return dates (especially Grand Ronde), while others showed some bimodal timing behavior (e.g., Imnaha). Although return year was a significant factor affecting run timing based on linear regression, no clear pattern of origin, juvenile migration history, return year, or rear type helped explain the remaining bimodality.

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Figure 2. Distribution density of first-detection dates at Bonneville (blue) and McNary

Dam (green) for tagged fish from MPGs and individual populations from the Snake river spring/summer and Upper Columbia River spring run Chinook salmon ESUs. Small dotted vertical lines indicate median arrival date at Bonneville (left) and McNary (right). Long dash shows 15 June as a reference date. Solid black bars represent means. Numbers at right reflect proportions from each group that passed McNary Dam after 15 June.

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Figure 3. Distribution density of the arrival dates at Bonneville Dam. Shaded areas represent estimated distributions, and lines show mean and median arrival dates, as in Figure 2. The number in the right column reflects the proportion of each tag group that passed Bonneville Dam after 15 June.

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Summarystatistics

For combined groups of tagged Chinook salmon adults originating from the Upper Columbia River ESU, median date of arrival at Bonneville Dam was 3 May (SD 15.4 d). For tagged adults from the Snake River ESU overall, median date of arrival was 8 May (8.1 d) for early groups and 2 Jun (14.6 d) for late groups. Arrival dates at McNary Dam formed a pattern similar to that observed at Bonneville Dam, but 5-7 d later (Table 7). Arrival timing at Bonneville Dam was significantly earlier for tagged fish from the Upper Columbia ESU than for tagged early-migrants from the Snake River ESU (Χ2

1=377.2, P<0.001). Early Snake River fish were in turn significantly earlier than late Snake River fish (Χ2

1 = 3018.6, P <0.001). For tagged fish from the Lower Snake River MPG, the median arrival date at Bonneville was 5 d to 5 weeks earlier than for other Snake River fish (Table 7a-b). This group had the most compact window of migration dates within the ESU (SD 11 d for hatchery, 13 d for wild fish; Figure 2; Table 7a-b). Fish from the Grande Ronde River MPG (excluding Imnaha) also had an early median migration date, but displayed a protracted migration (SD 18 and 20 d for hatchery and wild, respectively). Timing of fish from the Middle Fork Salmon River and Upper Salmon River MPGs (excluding Pahsimeroi) overlapped closely with that of fish from the Grande Ronde River MPG (excluding Imnaha). Each of these early migrant groups were significantly different from each other, with the possible exception of Middle Fork and Upper Salmon early (Χ2

1 = 3.17, P = 0.07).

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Table 7a. Arrival time statistics of spring and spring/summer Chinook salmon to Bonneville Dam by tag group. Numbers of tagged fish released are shown, along with the number and percent that passed Bonneville Dam after 15 June. Also shown are the standard deviations of the migration period percentile passage dates at Bonneville. Shading indicates median arrival dates.

Adult spring and spring/summer Chinook passage at Bonneville Dam

Fish Passage released after 15 June Passage percentile (date) Tag group (n) (n) (%) sd 5th 25th 50th 75th 95th

Hatchery and wild fish combinedRapid River 5,856 6 0 10 13 Apr 20 Apr 27 Apr 4 May 14 MayClearwater 6,397 62 1 13 14 Apr 24 Apr 1 May 8 May 19 MayUpper Columbia run Methow 1,061 2 0 11 17 Apr 25 Apr 1 May 9 May 19 MayEntiat 6,85 18 3 15 17 Apr 25 Apr 3 May 10 May 4 JunWenatchee 3,316 89 3 17 16 Apr 24 Apr 3 May 14 May 8 JunSnake Spring run Lower Snake 2,94 2 1 12 18 Apr 26 Apr 2 May 9 May 24 MayGrande Ronde 2,478 118 5 19 16 Apr 28 Apr 7 May 24 May 14 JunMiddle Fork Salmon 5,19 26 5 17 21 Apr 2 May 11 May 28 May 14 JunUpper Salmon spring 882 53 6 17 22 Apr 4 May 14 May 29 May 16 JunSnake Summer run South Fork Salmon 4,671 725 16 14 9 May 20 May 1 Jun 10 Jun 23 JunImnaha 2,276 496 22 15 7 May 24 May 4 Jun 13 Jun 24 JunPahsimeroi 376 98 26 16 7 May 26 May 7 Jun 15 Jun 29 Jun

Hatchery fish onlyRapid River 4,565 6 0 10 13 Apr 20 Apr 27 Apr 4 May 14 MayClearwater 4,481 50 1 12 14 Apr 24 Apr 1 May 8 May 20 MayUpper Columbia run Methow 818 2 0 11 17 Apr 24 Apr 1 May 8 May 17 MayEntiat 333 1 0 10 15 Apr 23 Apr 29 Apr 6 May 17 MayWenatchee 2267 40 2 15 15 Apr 23 Apr 1 May 10 May 3 JunSnake Spring run Lower Snake 130 0 0 11 15 Apr 25 Apr 2 May 8 May 17 MayGrande Ronde 1273 65 5 18 15 Apr 27 Apr 6 May 20 May 13 JunUpper Salmon spring 284 27 10 16 27 Apr 6 May 17 May 31 May 16 JunSnake Summer run South Fork Salmon 2,907 617 21 14 9 May 20 May 1 Jun 10 Jun 24 JunImnaha 1,106 352 32 14 11 May 27 May 6 Jun 14 Jun 25 JunPahsimeroi 206 69 33 16 7 May 26 May 6 Jun 14 Jun 26 Jun

Wild fish onlyRapid River 2 0 0 25 2 Apr 9 Apr 17 Apr 26 Apr 3 MayClearwater 460 12 3 20 15 Apr 23 Apr 1 May 8 May 16 MayUpper Columbia run Methow 102 0 0 12 18 Apr 29 Apr 5 May 12 May 30 MayEntiat 273 17 6 18 20 Apr 30 Apr 9 May 18 May 21 JunWenatchee 482 49 10 16 28 Apr 11 May 21 May 3 Jun 18 JunSnake Spring run Lower Snake 144 2 1 13 18 Apr 26 Apr 1 May 9 May 28 MayGrande Ronde 886 53 6 20 18 Apr 29 Apr 9 May 28 May 16 JunMiddle Fork Salmon 519 26 5 17 21 Apr 2 May 11 May 28 May 14 JunUpper Salmon spring 530 26 5 17 20 Apr 1 May 11 May 28 May 13 JunSnake Summer run South Fork Salmon 879 108 12 14 9 May 20 May 30 May 8 Jun 21 JunImnaha 793 144 18 17 2 May 19 May 1 Jun 12 Jun 23 JunPahsimeroi 96 29 30 18 9 May 24 May 7 Jun 16 Jun 6 Jul

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Table 7b. Arrival timing statistics of spring and spring/summer Chinook salmon to McNary Dam by tag group. Numbers of tagged fish released are shown with the percent passing after 15 June and standard deviation of the migration period. Shading indicates median arrival dates.

Tag group

Adult spring and spring/summer Chinook at McNary Dam Fish

released (n)

After15 June

(%) SD

Passage percentile (date)

5th 25th 50th 75th 95th

Hatchery and wild fish combinedRapid River 5,856 0 11 19 Apr 26 Apr 4 May 10 May 21 MayClearwater 6,397 2 12 21 Apr 2 May 8 May 14 May 28 MayUpper Columbia run Methow 1,061 1 11 23 Apr 1 May 8 May 14 May 24 MayEntiat 685 4 15 23 Apr 2 May 9 May 17 May 10 JunWenatchee 3,316 6 17 22 Apr 1 May 10 May 20 May 16 JunSnake Spring run Lower Snake 294 2 13 23 Apr 2 May 8 May 15 May 31 MayGrande Ronde 2478 10 19 22 Apr 4 May 13 May 31 May 22 JunMiddle Fork Salmon 519 11 18 28 Apr 8 May 18 May 3 Jun 22 JunUpper Salmon spring 882 13 17 29 Apr 9 May 19 May 4 Jun 23 JunSnake Summer run South Fork Salmon 4,671 30 14 15 May 27 May 7 Jun 16 Jun 30 JunImnaha 2,276 39 16 12 May 31 May 11 Jun 20 Jun 2 JulPahsimeroi 376 41 17 12 May 30 May 12 Jun 21 Jun 5 Jul

Hatchery fishRapid River 4,565 0 11 19 Apr 26 Apr 4 May 10 May 21 MayClearwater 4,481 2 12 21 Apr 2 May 8 May 15 May 28 MayUpper Columbia run Methow 818 1 11 23 Apr 1 May 7 May 14 May 23 MayEntiat 333 1 11 22 Apr 30 Apr 7 May 12 May 26 MayWenatchee 2,267 3 15 22 Apr 30 Apr 8 May 16 May 11 JunSnake Spring run Lower Snake 130 0 11 21 Apr 2 May 8 May 15 May 23 MayGrande Ronde 1,273 8 18 21 Apr 3 May 12 May 29 May 20 JunUpper Salmon spring 284 13 16 3 May 11 May 23 May 5 Jun 22 JunSnake Summer run South Fork Salmon 2,907 31 15 15 May 27 May 7 Jun 17 Jun 30 JunImnaha 1,106 42 14 17 May 2 Jun 12 Jun 21 Jun 3 JulPahsimeroi 206 41 17 12 May 30 May 12 Jun 21 Jun 4 Jul

Wild FishRapid River 2 0 20 14 Apr 20 Apr 27 Apr 4 May 10 MayClearwater 460 2 14 21 Apr 30 Apr 7 May 14 May 22 MayUpper Columbia run Methow 102 2 13 24 Apr 3 May 10 May 17 May 5 JunEntiat 273 9 18 28 Apr 5 May 14 May 24 May 30 JunWenatchee 482 19 17 4 May 17 May 28 May 9 Jun 26 JunSnake Spring run Lower Snake 144 4 14 23 Apr 1 May 7 May 15 May 6 JunGrande Ronde 886 13 20 24 Apr 5 May 15 May 3 Jun 24 JunMiddle Fork Salmon 519 11 18 28 Apr 8 May 18 May 3 Jun 22 JunUpper Salmon spring 530 12 18 26 Apr 7 May 18 May 4 Jun 23 JunSnake Summer run South Fork Salmon 879 29 14 14 May 28 May 7 Jun 16 Jun 28 JunImnaha 793 34 17 8 May 25 May 7 Jun 18 Jun 2 JulPahsimeroi 96 41 17 13 May 29 May 12 Jun 20 Jun 6 Jul

20

Comparisonsbyrearingtypeandorigin

Within-year variability of median arrival at Bonneville was generally lower in hatchery fish compared with wild fish, and lower for fish from the Upper Columbia and Lower Snake than other Snake River fish (Table 7a). All runs had statistically different run timing for hatchery vs. wild fish. These differences were much larger in tagged fish from the Upper Columbia ESU than in those from the Snake River ESU. The discrepancy between hatchery and wild migration timing was greatest for fish from the Wenatchee River, where the interquartile range did not overlap (Figure 4). Median migration date for hatchery fish was 20 April for Entiat fish and 2 May for Methow and Wenatchee fish. Median migration date for wild fish was 5 May (Methow), 9 May (Entiat), and 22 May (Wenatchee). Hatchery fish from the Upper Salmon MPG (early, excluding Pahsimeroi), South Fork Salmon River MPG, and Imnaha River arrived slightly later than did wild fish from these groups. Figure 4. Arrival day at Bonneville (BO, open boxes) and McNary (MN, shaded boxes)

Dam for wild (blue) and hatchery (green) fish from the three populations in the upper Columbia including all data from 2004 to 2015. Boxes show the interquartile range with the solid line within each box showing the median. Whiskers are 1.5 times beyond the interquartile range, with data beyond this range shown individually. A line at 15 June is shown for reference.

21

Migrationrate

The reach from Bonneville to McNary Dam is the first encountered by upstream migrant adults from both ESUs upon entering the hydrosystem. Travel time within this reach varied among years for both populations (Table 8a-c). Among all years combined, travel rates (km/d) between Bonneville and McNary Dam were significantly different between Snake River early and late groups (P = 0.03), although the difference was less than one day. In most years, late fish swam slightly slower than early fish in either ESU (Figure 5). No significant differences in travel rates were found for upper Columbia and Snake River early runs within this reach (mean, 6 d; P = 0.25). Across years, tagged fish from the Snake River spring/summer run Chinook salmon ESU took about 14 d on average to migrate from Bonneville to Lower Granite Dam. Again, travel time was about one day longer, on average for late than for early populations. For upper Columbia fish, mean cumulative passage from Bonneville to Rock Island Dam was approximately 16 d. Figure 5. Rates of travel from Bonneville to McNary Dam for returning adults from the

Upper Columbia spring run and Snake River spring/summer run Chinook salmon ESUs, 2004-2014.

25.0

30.0

35.0

40.0

45.0

50.0

2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

Migration rate (km

/d) 

Snake, spring run

Snake, summer run

Upper Columbia

22

Table 8a. Median travel time and migration rate between dam and through the entire hydrosystem from Bonnville to Rock Island Dam for tagged fish from the Upper Columbia River spring run Chinook salmon ESU, 2004-2014.

Upper Columbia River spring run Chinook salmon

Bonneville to McNary

(238 km) McNary to Priest Rapids

(169 km) Priest Rapids to Rock Island

(89 km) Bonneville to Rock Island

(496 km)

Year N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d)

2004 689 5.2 45.8 547 5.0 33.8 244 6.2 14.4 286 18.0 27.6 2005 662 5.9 40.3 574 4.4 38.4 414 4.2 21.2 471 16.1 30.8 2006 510 6.3 37.8 494 3.9 43.3 437 4.1 21.7 441 15.0 33.1 2007 77 6.1 39.0 79 5.4 31.3 74 4.5 19.8 71 17.6 28.2 2008 88 6.0 39.7 88 4.9 34.5 85 3.7 24.1 84 16.0 31.0 2009 104 5.9 40.3 101 4.0 42.3 95 3.3 27.0 96 13.9 35.7 2010 374 5.5 43.3 396 4.3 39.3 359 3.1 28.7 359 13.6 36.5 2011 251 7.0 34.0 246 5.1 33.1 221 3.6 24.7 219 18.5 26.8 2012 393 6.1 39.0 311 5.1 33.1 300 3.0 29.7 373 15.0 33.1 2013 213 5.8 41.0 217 5.6 30.2 204 3.0 29.7 200 15.5 32.0 2014 309 6.1 39.0 304 4.4 38.4 229 4.2 21.2 230 16.2 30.6

Overall 3,670 5.9 40.3 3,357 4.5 37.6 2,662 3.9 22.8 2,830 15.7 31.6

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Table 8b. Median travel time and migration rate through individual reaches and through the entire hydrosystem from Bonneville to Lower Granite Dam for early vs. late-run groups of tagged fish from the Snake River spring/summer run Chinook salmon ESU.

Year

Snake River Chinook salmon migration rates by run-timing group

Bonneville to McNary (238 km)

McNary to Ice Harbor (68 km)

Ice Harbor to Lower Granite (157 km)

Bonneville to Lower Granite (462 km)

N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d)

Early run (spring) 2004 199 5.8 41.0 200 1.4 48.7 198 3.9 40.3 194 12.0 37.02005 104 5.7 41.8 108 1.9 36.3 103 4.8 32.7 97 13.7 36.42006 64 6.1 39.0 64 1.8 37.8 61 5.2 30.2 60 15.6 28.92007 56 5.9 40.3 56 1.8 37.3 55 5.1 30.8 53 13.6 32.82008 159 6.3 37.8 153 1.9 35.6 150 5.1 30.8 151 14.9 28.72009 237 5.5 43.3 237 1.7 39.9 221 4.7 33.4 218 13.0 33.22010 665 5.1 46.7 658 1.6 43.5 597 5.8 27.1 594 13.7 30.62011 529 6.0 39.7 516 1.9 36.6 458 7.0 22.4 465 17.8 24.32012 359 6.0 39.7 357 1.7 39.6 316 4.3 36.5 311 12.6 33.52013 216 5.6 42.5 214 1.5 46.2 172 4.6 34.1 170 12.7 35.32014 336 5.7 41.8 334 1.7 39.4 304 4.8 32.7 302 12.7 32.5

Overall 2,924 5.7 41.8 2,897 1.7 40.0 2,635 4.8 32.7 2,615 13.7 33.7

Late run (summer) 2004 560 5.8 41.0 567 1.7 39.2 561 3.9 40.3 550 12.5 37.02005 396 5.7 41.8 369 1.6 42.4 351 4.2 37.4 348 12.7 36.42006 224 6.8 35.0 224 1.5 44.1 205 5.9 26.6 204 16.0 28.92007 244 6.0 39.7 243 1.8 38.9 229 4.8 32.7 229 14.1 32.82008 538 8.0 29.8 533 1.9 35.7 516 4.8 32.7 516 16.1 28.72009 504 6.2 38.4 498 1.8 37.1 481 4.7 33.4 483 13.9 33.22010 967 5.5 43.3 952 1.9 36.2 926 4.8 32.7 932 15.1 30.62011 568 8.0 29.8 549 1.9 35.4 517 6.5 24.2 532 19.0 24.32012 483 6.5 36.6 478 1.8 36.8 464 4.7 33.4 465 13.8 33.52013 269 6.0 39.7 267 1.9 36.6 253 4.7 33.4 252 13.1 35.32014 348 5.9 40.3 342 1.8 36.9 329 5.0 31.4 329 14.2 32.5

Overall 5,101 6.3 37.8 5,022 1.8 37.8 4,832 4.8 32.7 4,840 14.8 31.2

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Table 8c. Median travel time and migration rate time through individual reaches and through the entire hydrosystem from Bonneville to Lower Granite Dam for tagged fish from the Snake River spring/summer run Chinook salmon ESU (early and late run combined), 2004-2014.

Snake River spring/summer run Chinook salmon—combined early and late-run fish

Bonneville to McNary

(238 km) McNary to Ice Harbor

(68 km) Ice Harbor to Lower Granite

(157 km) Bonneville to Lower Granite

(462 km)

Year N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d) N Travel

time (d) Rate

(km/d)

2004 759 5.8 41.0 767 1.7 40.5 759 3.9 40.3 744 12.3 37.6

2005 473 5.7 41.8 477 1.7 40.3 454 4.4 35.7 445 12.9 35.8

2006 288 6.6 36.1 288 1.6 42.1 266 5.8 27.1 264 15.9 29.1

2007 300 6.0 39.7 299 1.8 38.3 284 4.9 32.0 282 13.9 33.2

2008 697 7.8 30.5 686 1.9 35.7 666 5.0 31.4 667 15.9 29.1

2009 741 6.0 39.7 735 1.8 37.8 702 4.7 33.4 701 13.8 33.5

2010 1,632 5.3 44.9 1,610 1.8 38.0 1,523 5.6 28.0 1,526 14.6 31.6

2011 1,097 7.2 33.1 1,065 1.9 36.1 975 6.5 24.2 997 18.4 25.1

2012 842 6.2 38.4 835 1.8 37.8 780 4.5 34.9 776 13.2 35.0

2013 485 5.8 41.0 481 1.7 39.0 425 4.6 34.1 422 13.0 35.5

2014 684 5.8 41.0 676 1.8 38.0 633 4.8 32.7 631 13.4 34.5

Overall 7,998 6.0 39.7 7,919 1.8 37.8 7,467 4.9 32.0 7,455 13.7 33.7

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Cumulative travel time for Snake River fish from Bonneville to Lower Granite Dam was longest for both early and late runs in 2011. Over this same reach, cumulative travel time was shortest (12 d) and migration rate most rapid (37 km/d) for both early and late Snake River fish in 2004. For Upper Columbia River fish, the shortest cumulative travel time from Bonneville to Rock Island Dam was 14 d in 2010. For both early and late tagged fish from the Snake River ESU, travel rates between Bonneville and McNary followed the same general pattern year-to-year as that of fish from the Upper Columbia ESU (Figure 5). One exception occurred in 2008, when late fish traveled much more slowly than average, while early fish in both ESUs were largely unaffected. For early Snake River Chinook salmon adults, travel rate decreased from 2010 to 2011. However, travel rate for this run remained well above that of late fish from both the Upper Columbia and Snake River late runs. Fish from the Upper Columbia ESU showed a relatively steady travel rate through the Bonneville-to-McNary reach. Migration rate for these fish was similar to that of Snake River early fish, peaking in 2010 at 43 km/d and dipping in 2011 to 34 km/d, with an increase the following year to 39 km/d. Effectsoftimingonharvestexposure

To describe the relative impact of migration timing on exposure to spring vs. summer harvest management periods on the different populations, we calculated the proportion of fish that passed McNary Dam before 15 June each year. Because this metric only counts fish that survived to pass McNary Dam, it does not reflect the impact of harvest within Zone 6. Nonetheless, it does provide a rough indicator of relative exposure to the summer harvest period. Over one-quarter of late-run populations passed McNary after 15 June, on average. The highest percentages occurred in the late-run and slow migration years of 2011 and 2007. Median travel time between Bonneville and McNary was slowest for Methow (6.05 d for hatchery, 6.2 d for wild fish), and longest for Wenatchee River fish (6.8 d for hatchery and 7.5 d for wild fish). For Wenatchee River fish, the additional travel time for the wild cohort indicated an even greater difference in Zone 6 harvest exposure than indicated by their later arrival timing at Bonneville. When we compared exposure to harvest only between wild vs. hatchery fish that passed McNary Dam, we found that the proportion of fish passing after 15 June was less than 3% for all hatchery populations, but was 9% for wild fish from the Entiat River and 19% for wild fish from the Wenatchee.

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Figure 6. Year effects in rank order: Day of McNary Dam arrival and distribution density of populations originating from the upper Columbia (top) Snake River ESU for earlier (bottom left) and later (bottom right) populations. Shaded area represents the estimated distribution density of each group. Individual observations are shown as points along the x-axis. The dotted vertical line represents median arrival date for all fish shown. Thick solid black lines represent mean arrival date for fish in each year, whereas the longer thin dotted line shows the median arrival day for all years, and the long solid line shows 15 June as a reference date.

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Table 9. Proportions of fish in each tag group that passed McNary Dam after 15 June 2004-2015. Mean, maximum, and minimum proportions over this period are shown by group. Shading indicates years during which the maximum proportion of adult fish passed during the summer harvest period.

Tag group Mean Min Max

Proportion that passed McNary Dam during summer harvest period

2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015

Imnaha 0.36 0.30 0.56 0.42 0.59 0.21 0.34 0.64 0.35 0.32 0.38 0.49 0.42 0.21 0.64

South Fork Salmon 0.11 0.28 0.58 0.42 0.45 0.17 0.28 0.59 0.32 0.29 0.22 0.35 0.34 0.11 0.59

Upper Salmon 0.22 0.13 0.17 0.43 0.30 0.27 0.24 0.37 0.38 0.32 0.2 0.25 0.27 0.13 0.43

Middle Fork Salmon 0.08 0.12 0.00 0.00 0.50 0.00 0.03 0.22 0.09 0.17 0.07 0.13 0.14 0.00 0.50

Grande Ronde 0.10 0.16 0.13 0.18 0.17 0.13 0.04 0.17 0.10 0.07 0.06 0.08 0.12 0.04 0.18

Entiat 0.00 0.00 0.02 0.05 0.00 0.00 0.03 0.09 0.12 0.42 0.05 0.07 0.09 0.00 0.42

Wenatchee 0.00 0.01 0.00 0 0.10 0.08 0.08 0.24 0.10 0.11 0.07 0.16 0.09 0.00 0.24

Methow 0.00 0.01 0.01 0.17 0.00 0.00 0.00 0.04 0.01 0.00 0.02 0.00 0.03 0.00 0.17

Lower Snake 0.00 0.00 -- -- 0.00 0.00 0.00 0.09 0.00 0.00 0 0.04 0.02 0.00 0.09

Clearwater 0.00 0.00 0.04 0.03 0.02 0.01 0.00 0.02 0.00 0.02 0.03 0.02 0.02 0.00 0.04

Rapid River 0.00 0.00 0.01 0.00 0.01 0.00 0.00 0.01 0.01 0.00 0.01 0.00 0.00 0.00 0.01

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AdultMigrationSurvival

Methods To estimate survival, we constructed a PIT-tag detection history for each fish in every year for which detection data were available from 2004 to 2015. Each detection history was comprised of a series of binary codes indicating passage (1) or non-passage (0) at each dam encountered during the upstream migration. We conducted a mark-recapture analysis based on individual detection histories, with detections used as recaptures. We then estimated detection efficiency and survival between major reaches using the Cormack-Jolly-Seber (CJS) model with Survival Under Proportional Hazards (SURPH) software (Lady et al. 2001). For fish from the Columbia River ESU, each detection history indicated whether or not the fish was detected at Bonneville, McNary, Priest Rapids, and Rock Island Dam. For fish from the Snake River ESU, detection histories indicated whether detection occurred at Bonneville, McNary, Ice Harbor, and Lower Granite Dam. In 2013, adult PIT detectors were installed at The Dalles Dam. Thus, an additional digit was added to the detection history of each fish from 2013 to 2015. The last point of detection for these estimates was Rock Island Dam for Upper Columbia fish and Lower Granite Dam for Snake River fish. To estimate detection efficiency at these points, we needed at least some detection data from sites upstream. These data were available for most years from monitors at upstream dams and instream monitors in spawning tributaries. The number of PIT-tag monitoring systems has increased rapidly over the past decade. However, in the early years of the study, upstream detection numbers were insufficient for estimates of detection efficiency at Lower Granite Dam (before 2008) and at Rock Island Dam (before 2011). For estimates of detection efficiency, we used all fish detected at a given dam. However, for estimates of survival, we used only fish detected at Bonneville Dam. For fish from the Upper Columbia River ESU, we estimated survival from Bonneville to Rock Island Dam, which is the last major dam these adult fish encounter before the Wenatchee population leaves the mainstem. For fish from the Snake River ESU, we estimated survival from Bonneville to

29

Lower Granite Dam. Fish from the Lower Snake MPG were excluded from these estimates because the Tucannon River confluence with the Snake River is downstream of Lower Granite Dam. ComparisonsfromBonnevilletoMcNaryDam

All Chinook salmon groups and populations in both the Upper Columbia and Snake River ESUs pass through the reach from Bonneville to McNary Dam. As of 2013, this reach included four dams with PIT-monitoring systems in the adult ladders. Therefore, this was the primary reach used to compare tag groups from both ESUs. Within this reach, we calculated survival for each ESU as a whole and also compared survival for 1) hatchery vs. wild fish, 2) fish with transported vs. inriver juvenile migration histories, 3) early vs. late-run populations/groups and 4) wild fish with inriver juvenile migration histories from the Upper Columbia vs. early Snake River groups. We also report survival by MPG or population for as many years as possible (those with at least 10 fish), although sample sizes were insufficient for these estimates in some years. We compared groups using Student’s t test paired by year. Juveniletransportgroups

A subset of fish with a juvenile migration history of transport existed in every adult return year examined for fish from the Snake River ESU. However, for the Upper Columbia ESU, such a subset of transported fish existed only from 2004 to 2007. To identify transported fish, the route of passage was determined for PIT-tagged juvenile salmon arriving at "collector" dams, or dams with transport holding raceways and barge-loading facilities. To be transported, a fish first had to be guided into the juvenile bypass system at a collector dam. Within the bypass system, the subset of fish determined to have been transported included only fish that were last detected on a monitor leading to a transport holding raceway. We used PTAGIS interrogation summary reports to help identify routes of dam passage for tagged fish guided into bypass systems as juveniles. Based on last monitor name and detection date within these reports, the route of passage (i.e., returned to river, transport, removals, or unknown) was assigned. Route designations were as follows: Transport: Fish was last detected on monitors leading to a transport holding raceway.

30

Removal: Removals included mortalities at dams, which were neither transported nor returned to river. Further information on mortalities can be gathered from PTAGIS database queries. Removals also included fish with last detections on the sample room or sample tank monitors. These fish were usually transported, but we classed them as removals due to possible handling effects;

Unknown: Fish with last detections on monitors that did not indicate a specific route of passage. For example, a fish last detected on a monitor located mid-way through the bypass system (such as at the separator) could have been returned to river, transported, or removed (e.g., mortality).

Returned to River: The last antenna group name was none of the above.

Identification of juvenile migration history can be complex, and information based on the last detection on a particular PIT-tag monitor can be misleading, due to unforeseen circumstances at the dam. For example, fish collected in a raceway may be held for a maximum of 48 h before loading for transport. If a transport barge is delayed, collected fish may need to be returned to the river. Fish collected in transport holding raceways may also need to be released to the river during periods of high fish density or because of mechanical failures, etc. Therefore, data from PTAGIS interrogation summaries could include cases of fish with detections that indicated transport but that had actually been returned to the river from a transport holding raceway. We consulted with on-site biologists from the U.S. Army Corps of Engineers biologists to determine when such incidents had occurred. Care was taken to identify these special cases and use the information to correct fish passage routes within the dataset. After identifying juvenile passage routes, a binary code was assigned to each fish, with 1 indicating transport and 0 indicating inriver migration.

31

Results Comparisonsbyoriginandjuvenilemigrationhistory

In comparing estimated survival from Bonneville to McNary Dam among tagged groups from both ESUs, two factors emerged as significant effects. First, hatchery fish had lower estimated survival than wild fish (Table 10; Figure 7). For fish from the Snake River ESU, mean estimated survival for was 0.79 for hatchery vs. 0.84 for wild groups over all years (t11 = -3.92, P = 0.002). For fish from the Upper Columbia ESU, estimated survival was 0.81 for hatchery vs. z0.84 for wild fish (t10 = -2.53, P = 0.03). Second, for fish from the Snake River ESU, transported groups had lower mean estimated survival (0.79) than inriver migrants (0.81) over all years (Table 10), but the difference was only 2% on average (t11 = 2.42, P = 0.034). There was no significant effect of transportation on tagged fish from the Upper Columbia ESU (Figure 8). After accounting for these two factors by comparing only wild fish that had not been transported, there was no difference between Upper Columbia and Snake River early runs (mean for both was 0.84).

32

Table 10. Estimated survival (mean and SE) with numbers of fish for ESUs overall and for various subsets of each ESU. Dashes indicate that data was insufficient for survival estimates.

Inriver migrant wild fish Snake River Snake River ESU Upper Columbia ESU

Year Snake River Upper Columbia Inriver Transport Hatchery Wild Hatchery Wild

Mean estimated survival 2004 0.91 (0.037) -- 0.84 (0.015) 0.79 (0.024) 0.81 (0.014) 0.88 (0.025) 0.85 (0.013) -- 2005 0.97 (0.033) -- 0.92 (0.015) 0.89 (0.022) 0.91 (0.014) 0.92 (0.031) 0.82 (0.014) -- 2006 0.86 (0.094) -- 0.79 (0.033) 0.79 (0.028) 0.77 (0.026) 0.84 (0.037) 0.79 (0.016) 0.83 (0.152) 2007 -- -- 0.82 (0.04) 0.85 (0.022) 0.85 (0.021) 0.81 (0.046) 0.81 (0.042) 0.86 (0.132) 2008 0.84 (0.051) 0.87 (0.06) 0.84 (0.018) 0.86 (0.017) 0.85 (0.014) 0.86 (0.026) 0.76 (0.047) 0.87 (0.06) 2009 0.85 (0.036) 0.78 (0.068) 0.85 (0.014) 0.86 (0.022) 0.85 (0.015) 0.88 (0.02) 0.84 (0.039) 0.78 (0.068) 2010 0.84 (0.022) 0.87 (0.024) 0.83 (0.011) 0.79 (0.015) 0.8 (0.011) 0.84 (0.013) 0.79 (0.025) 0.87 (0.024) 2011 0.83 (0.022) 0.83 (0.027) 0.71 (0.014) 0.7 (0.021) 0.68 (0.016) 0.74 (0.017) 0.75 (0.039) 0.82 (0.027) 2012 0.82 (0.033) 0.87 (0.029) 0.84 (0.013) 0.81 (0.027) 0.82 (0.016) 0.88 (0.016) 0.82 (0.021) 0.87 (0.029) 2013 0.92 (0.025) 0.9 (0.039) 0.87 (0.016) 0.78 (0.037) 0.82 (0.022) 0.89 (0.018) 0.84 (0.026) 0.9 (0.039) 2014 0.78 (0.028) 0.84 (0.042) 0.72 (0.016) 0.69 (0.035) 0.69 (0.02) 0.76 (0.021) 0.86 (0.02) 0.84 (0.042) 2015 0.81 (0.025) 0.77 (0.041) 0.7 (0.014) 0.62 (0.026) 0.64 (0.015) 0.78 (0.02) 0.8 (0.019) 0.77 (0.041)

Mean 0.84 0.84 0.81 0.79 0.79 0.84 0.81 0.84 Number of fish used to estimate survival 2004 64 0 647 301 767 182 836 1 2005 35 7 337 209 455 91 832 7 2006 15 6 153 216 272 97 660 13 2007 9 7 95 269 289 75 91 17 2008 52 31 431 398 658 172 86 31 2009 103 37 626 256 624 259 91 55 2010 281 196 1,274 750 1,281 751 264 207 2011 284 200 1,075 500 887 703 128 207 2012 135 134 810 216 631 419 348 146 2013 119 60 448 129 305 284 204 66 2014 223 76 799 176 561 430 315 101 2015 253 107 1,126 352 1,038 440 447 107

33

Figure 7. Snake and upper Columbia River survival from Bonneville (BON) to McNary

(MCN) dams by rear type (hatchery and wild). Shaded area represents ±1 SE.

34

Figure 8. Survival from Bonneville to McNary Dam for transported vs. inriver-migrant

Snake River spring/summer Chinook salmon Shaded areas represent ±1 SE.

35

SurvivalfromBonnevilletoMcNaryDamforSnakeRiverFish

At dams equipped with PIT-tag monitoring systems in the fishways, estimated detection efficiency for adult fish was over 98% at all dams after 2006, except at Ice Harbor Dam in 2011, when detection efficiency dropped slightly, to 96.5% (Table 11). Table 11. Mean detection probability (and SE) by dam for adult Snake River

spring/summer Chinook salmon tagged as juveniles. Dashes indicate data was not available to estimate detection probability.

Year Bonneville The Dalles McNary Ice Harbor Lower Granite

2004 97.1 (0.6) -- 99.9 (0.1) 99.3 (0.3) --

2005 95.2 (1) -- 99.6 (0.3) 97.5 (0.7) --

2006 98.3 (0.8) -- 100.0 (0) 99.2 (0.5) --

2007 98.4 (0.7) -- 99.3 (0.5) 99.6 (0.4) --

2008 98.7 (0.4) -- 99.9 (0.2) 98.8 (0.4) --

2009 98.4 (0.5) -- 99.6 (0.2) 98.9 (0.4) 100.0 (0)

2010 98.8 (0.3) -- 99.8 (0.1) 98.8 (0.3) 100.0 (0)

2011 98.5 (0.4) -- 99.5 (0.2) 96.5 (0.6) 98.8 (0.4)

2012 98.3 (0.4) -- 99.8 (0.2) 99.2 (0.3) 98.9 (0.5)

2013 99.1 (0.4) 99.8 (0.2) 99.8 (0.2) 99.8 (0.2) 100.0 (0)

2014 99.3 (0.3) 99.9 (0.1) 99.7 (0.2) 99.7 (0.2) 100.0 (0)

2015 98.1 (0.3) 100.0 (0) 99.9 (0.1) 99.2 (0.3) 100.0 (0)

Average 98.7 (0.5) 99.9 (0.1) 99.7 (0.2) 98.9 (0.4) 99.7(0.2)

For tagged adults from the Snake River ESU, estimated survival from Bonneville to Lower Granite Dam ranged from a low of 65% in 2015 to a high of over 90% in 2005. Mean estimated survival for these fish was 79.6% over the 12-year period from 2004 to 2015, and the majority of losses occurred within the reach from Bonneville to McNary Dam (Table 12). Survival of fish from this ESU was below 80% in both the reach from Bonneville to McNary Dam and over the entire hydrosystem from Bonneville to Lower Granite in 2006, 2011, 2014 and 2015.

36

In the reaches from McNary to Ice Harbor and from Ice Harbor to Lower Granite Dam, survival for tagged adults from the Snake River spring/summer run Chinook salmon ESU averaged 94% from the period 2004-2015. During this period, estimated survival for these fish dropped below 90% just once in the reach from McNary to Lower Granite Dam (88% in 2015). Table 12. Survival rates (mean and SE) for all Snake River spring/summer Chinook

salmon tagged as juveniles. Dashes indicate data was not available to estimate survival.

Year Bonneville to

McNary Bonneville

to The Dalles The Dalles to McNary

McNary to Ice Harbor

Ice Harbor to Lower Granite

Bonneville to Lower Granite

2004 82.1 (1.3) -- -- 99.1 (0.4) 98.8 (0.4) 81.4 (1.3)

2005 90.9 (1.3) -- -- 99.3 (0.4) 95.0 (1) 90.3 (1.3)

2006 79.1 (2.1) -- -- 99.7 (0.4) 91.9 (1.6) 78.9 (2.1)

2007 83.8 (1.9) -- -- 99 (0.6) 94.3 (1.4) 83.0 (2)

2008 85.1 (1.2) -- -- 98.6 (0.5) 97.1 (0.7) 83.9 (1.3)

2009 85.6 (1.2) -- -- 98.9 (0.4) 96.5 (0.7) 84.7 (1.2)

2010 81.6 (0.9) -- -- 98.8 (0.3) 97.0 (0.4) 80.6 (0.9)

2011 70.4 (1.2) -- -- 99.1 (0.3) 93.4 (0.8) 69.8 (1.2)

2012 84.0 (1.2) -- -- 98.6 (0.4) 96.9 (0.6) 82.8 (1.2)

2013 85.1 (1.5) 92.7 (1.1) 92.2 (1.2) 98.5 (0.6) 96.0 (0.9) 83.8 (1.6)

2014 71.5 (1.5) 83.7 (1.2) 86 (1.2) 98.4 (0.5) 96.6 (0.7) 70.4 (1.5)

2015 66.9 (1.3) 83.8 (1) 81 (1.1) 97.3 (0.5) 90.9 (1) 65.0 (1.3)

Average 80.5 (1.4) 86.7 (1.1) 86.4 (1.2) 98.8 (0.4) 95.4 (0.8) 79.6 (1.4)

37

Estimated survival for Snake River salmon varied across years within each tag group, but much of this variation could have been caused by small sample sizes at the population level (Figure 9, Table 13). Small sample sizes result from either fewer interrogation systems in earlier years or smaller numbers of juvenile fish tagged. For tagged adults from the Lower Snake River MPG, the highest 5-year mean survival estimate was 87% for years 2009-2015. Estimated survival for these fish was especially high in 2015, at 93%. Mean survival ranged 82-84% for early-run adults from the Lower Snake River, Grande Ronde River (excluding Imnaha), Upper Salmon River (excluding Pahsimeroi), and Middle Fork Salmon River MPGs. Mean survival ranged 75-79% for late-run adults from the South Fork Salmon River MPG, Imnaha River group, and Pahsimeroi River group (Table 13). In late-run groups, lower survival occurred largely in 3 years: 2011, 2014, and 2015. In these years, survival of late-run adults ranged 61-67%, whereas survival of early run adults ranged 78-79%. However, overall the difference in survival over these years between early and late-run fish was not statistically significant (t11 = 1.7159, P = 0.11). Figure 9. Snake River Chinook survival by tag group. Letters are ordered by median

arrival day at Bonneville Dam. Red letters designate late-run populations while blue letters designate early run. Solid black line shows the average across populations by year.

38

Table 13. Survival of early Snake River tag groups, i.e., those from the Lower Snake, Grande Ronde, Middle Fork Salmon, and Upper Salmon River. The second group consists of late-run Snake River group, i.e., those from the South Fork Salmon, Imnaha, and Pahsimeroi Rivers. The final two columns show combined survival and counts of those tag groups after they have been grouped into early and late-run categories.

Early-run Late-run Combined total

Year Lower Snake

Grande Rondea

Middle Fork

SalmonUpper

Salmonb

South Fork

Salmon Imnaha Pahsimeroi Early Late Adult survival rates

2004 -- 0.87 0.80 0.82 0.80 0.83 -- 0.86 0.81 2005 -- 0.90 -- 1.00 0.92 0.88 -- 0.92 0.91 2006 -- 0.77 -- 0.85 0.79 0.82 -- 0.78 0.79 2007 -- 0.88 -- 0.79 0.86 0.73 -- 0.86 0.83 2008 -- 0.77 -- 0.88 0.88 0.85 -- 0.79 0.87 2009 0.83 0.85 0.85 0.84 0.86 0.86 -- 0.85 0.86 2010 0.82 0.84 0.81 0.83 0.81 0.80 0.81 0.83 0.81 2011 0.89 0.78 0.80 0.79 0.65 0.65 0.63 0.79 0.65 2012 0.84 0.81 0.83 0.84 0.84 0.88 0.88 0.82 0.86 2013 0.89 0.83 0.89 0.91 0.87 0.77 0.75 0.87 0.84 2014 0.86 0.76 0.75 0.84 0.67 0.63 0.78 0.79 0.67 2015 0.93 0.78 0.82 0.74 0.61 0.62 0.62 0.78 0.61

Mean 0.87 0.82 0.82 0.84 0.79 0.78 0.75 0.83 0.79 Number of adult fish detected (n) 2004 2 199 15 22 539 168 4 238 711 2005 3 97 9 13 298 125 1 122 424 2006 0 70 1 13 189 91 5 84 285 2007 0 52 1 14 233 61 3 67 297 2008 2 162 4 33 494 130 5 201 629 2009 13 162 13 99 411 176 9 287 596 2010 62 481 143 127 637 479 103 813 1,219 2011 38 421 121 95 401 405 109 675 915 2012 46 268 64 97 334 224 17 475 575 2013 47 101 46 71 226 86 12 265 324 2014 30 236 56 120 375 124 50 442 549 2015 59 277 56 204 598 226 58 596 882

a Excluding Imnaha River b Excluding Pahsimeroi River

39

SurvivalfromBonnevilletoRockIslandDamforColumbiaRiverFish

Mean detection efficiency was 98% at Bonneville, 99% at McNary, and 100% at The Dalles Dam (Table 14). Mean detection efficiency was also near 99% at Priest Rapids Dam in most years. In 2012 however, 66 fish were detected upstream from Priest Rapids Dam without having been detected at the dam. Detection efficiency at Rock Island Dam has been variable in recent years, with lows of 73% in 2014 and 78% in 2015. Table 14. Detection probability (mean and SE) for the Upper Columbia ESU. Dashes

indicate that data for estimates was insufficient or unavailable.

Year Bonneville The Dalles McNary Priest Rapids Rock Island

2006 98.3 (0.5) -- 99.6 (0.3) 96.5 (0.9) 91.6 (2.0)

2007 96.8 (1.8) -- 100.0 (0.0) 100.0 (0.0) 92.9 (4.9)

2008 98.2 (1.2) -- 97.8 (1.6) 98.8 (1.2) 92.5 (4.2)

2009 100.0 (0.0) -- 99.0 (1.0) 99.0 (1.0) 93.4 (3.2)

2010 98.7 (0.5) -- 99.7 (0.3) 99.2 (0.5) 98.3 (0.8)

2011 97.9 (0.8) -- 97.6 (1.0) 98.7 (0.7) 87.9 (2.3)

2012 99.2 (0.4) -- 99.5 (0.4) 79.1 (2.1) 96.1 (1.0)

2013 98.1 (0.9) 100.0 (0.0) 99.1 (0.7) 99.5 (0.5) 95.7 (1.4)

2014 99.6 (0.2) 100.0 (0.0) 99.1 (0.5) 99.3 (0.5) 73.4 (2.5)

2015 98.1 (0.2) 100.0 (0.0) 100.0 (0.0) 96.3 (1.0) 78.3 (2.0)

Average 98.2 (0.2) 100.0 (0.0) 99.2 (0.6) 94.5 (1) 88.9 (3.9)

40

Table 15. Survival rates (mean and SE) for the Upper Columbia ESU. Dashes indicate that data for estimates was insufficient or unavailable.

Year Bonneville to McNary

Bonneville to The Dalles

The Dalles to McNary

McNary to Priest Rapids

Priest Rapids to Rock Island

Bonneville to Rock Island

2006 78.5 (1.6) -- -- 98.1 (0.7) 95.8 (1.8) 73.8

2007 81.1 (4.0) -- -- 98.7 (1.3) 100.0 (4.3) 80.0

2008 79.0 (3.8) -- -- 98.9 (1.1) 100.0 (4.9) 78.1

2009 82.0 (3.4) -- -- 98.1 (1.4) 100.0 (17.1) 80.4

2010 82.7 (1.8) -- -- 98.7 (0.6) 98.9 (1.3) 80.7

2011 78.9 (2.3) -- -- 98.1 (0.9) 100.0 (3.9) 77.4

2012 83.3 (1.7) -- -- 99.1 (0.7) 100.0 (1.4) 82.6

2013 85.2 (2.2) 91.1 (1.8) 93.6 (1.6) 99.6 (0.5) 99.5 (2.2) 84.4

2014 85.9 (1.8) 90.7 (1.5) 94.6 (1.2) 98.6 (0.7) 96.4 (2.6) 81.6

2015 79.3 (1.7) 90 (1.3) 88.1 (1.5) 99.0 (0.6) 98.8 (2.2) 77.6

Average 81.9 (2.2) 90.6 (1.5) 92.1 (1.4) 98.3 (0.9) 99.1 (5.3) 79.7

Mean survival of Upper Columbia ESU fish within the Bonneville to McNary reach was 82%. Mean cumulative survival, from Bonneville to Rock Island Dam was 80% and ranged from a low of 74% in 2006 to a high of 84% in 2013. Survival above McNary (McNary to Rock Island) was over 94% in all years. Survival differences between wild and hatchery fish were evident: wild-reared fish exhibited significantly higher survival (84%) compared to hatchery-reared fish (81%, t10 = -2.5334, P = 0.0297, Table 13; Figure 8). Yearly survival rates of Upper Columbia fish were driven by the most populous tag group, Wenatchee. Examining survival among tag groups within the upper Columbia ESU, no statistically significant difference was found among populations. Tagged fish with a juvenile history of transport did not have a detectable difference in survival rates across years. Although relatively few fish from the upper Columbia River were transported (387), they were transported over a shorter distance fish from the Snake River (from McNary Dam to Bonneville Dam), and transportation only affected adults returning in 4 years (2004-2007; P = 0.76).

41

Figure 10. Upper Columbia River -Chinook survival from Bonneville to McNary Dam

by for each population. Survival estimates are only shown when at least 20 fish were included in the estimate. Error bars represent ±1 SE.

42

FallbackandReascension

Methods During upstream migration, fish may ascend adult ladders but subsequently fall back downstream over hydrosystem dams. These fallback incidents may result in injury, mortality, migration delays, and/or bias in fishway counts. However, when relying on PIT-tag detection data, fallback events must be evaluated indirectly based on inferences from a series of detections (Burke et al. 2004). At least two detections are needed to infer directionality, and multiple detections are required to infer fallback and reascension. We estimated fallback rates using a program developed specifically to infer fallback from detections of PIT-tagged fish (Tiffani Marsh, NOAA Fisheries, personal communication). Fallback was assumed to have occurred only when we observed a particular sequence of detections, starting with the detection of a fish passing upstream through a fish ladder. Directional movement was confirmed by observing multiple detections within the ladder, with the final detection indicating upstream progress. Once upstream movement was confirmed, we could infer a fallback by observing additional detections indicating a) at least one subsequent passage attempt in a different ladder, or b) a delay of 6 h or more between passage attempts in the same ladder. The time criterion helped to distinguish a detection series that represented successful passage followed by fallback and reascension from one that represented upstream movement followed by vacillating directional movement within the ladder (i.e., upstream movement followed by downstream movement (without being detected) followed by further movement upstream (Burke et al. 2004). The time-based cutoff allowed us to separate records into distinct blocks. Specifically, if a series of detections was followed by a lack of detections for 6 h or more, it was classified as a block and considered separately from any following detections. If a block suggested upstream movement and ladder passage, we labeled the block as a successful passage event: any subsequent detections at that dam, regardless of position in the ladder, were interpreted as a separate ascension event (fallback and reascension). We used this method for analyses of fallbacks by adult Chinook salmon each dam and year for which data were available. We calculated both fallback rate (total fallback events ÷ unique fish passing × 100) and fallback percentage (number of unique fish that fell back ÷ total number of fish passing × 100) for each dam.

43

Results We calculated both fallback rate (total fallback events ÷ unique fish passing × 100) and fallback percentage (number of unique fish that fell back ÷ total number of fish passing × 100) for each dam. SnakeRiverSpring/SummerRunChinookSalmon

Fallback numbers and fallback rates for tagged Snake River fish varied greatly across years and dams (Table 16; Figures 11 and 12). Individual Snake River fish fell back 1-5 times. Of the Columbia River dams (Bonneville, The Dalles, McNary), McNary had the highest mean fallback rate (12.7, range 9.2-27.1) and highest mean probability of fallback (12%, range 9-25%). Of Snake River dams (Ice Harbor, Lower Granite), Lower Granite had the highest mean fallback rate (11.8, range 7.7-17.8) and highest mean probability of fallback (10%, range 7-15%). For dams with fallback data from years 2005-2014, the lowest fallback was Ice Harbor (mean fallback rate 5.2, mean fallback percent 5%). The Dalles Dam had the lowest mean fallback of all dams, but data was only available from 2013-14 (fallback rate 1.8, fallback percent 2%). Across years, the highest number of fallbacks for Snake River fish occurred in 2006. Fallback at McNary Dam in 2007 was extremely high, with a fallback rate of 27.1 and percent fallback of 25%. Other dams did not experience a similar spike in fallback that year. The year with the least amount of fallback was 2014, with a mean fallback rate of 7 and fallback percent of 7%. Transported Snake River fish had higher mean fallback rate and probability of fallback compared to in-river fish (transported: 11.5 fallback rate, 10% fallback probability; in-river: 9.5 fallback rate, 9% fallback probability). Examining overall differences in percent fallback by dam over time, transported fish had a higher percentage of fallback at most dams, especially after 2007 (Figure 13).

44

Table 16. Summary of fallbacks by dam for all tag groups from the Snake River spring/summer run Chinook salmon ESU.

Snake River spring/summer run Chinook salmon

Number of fish

passing (n) Number of fish that

fell back (n) Total number of

fallback events (n)Proportion of fallbacks (%)

Rate of fallback (%)

Bonneville Dam2005 522 28 33 5.4 6.3 2006 364 25 26 6.9 7.1 2007 359 44 47 12.3 13.1 2008 820 98 112 12.0 13.7 2009 870 104 116 12.0 13.3 2010 2004 193 208 9.6 10.4 2011 1,558 165 189 10.6 12.1 2012 1,015 111 125 10.9 12.3 2013 572 61 66 10.7 11.5 2014 971 100 107 10.3 11

The Dalles Dam2013 533 9 10 1.7 1.9 2014 815 13 13 1.6 1.6

McNary Dam2005 493 57 63 11.6 12.8 2006 291 29 29 10.0 10 2007 303 75 82 24.8 27.1 2008 706 65 74 9.2 10.5 2009 752 75 77 10.0 10.2 2010 1,649 143 152 8.7 9.2 2011 1,112 97 108 8.7 9.7 2012 858 89 91 10.4 10.6 2013 490 66 67 13.5 13.7 2014 698 91 92 13.0 13.2

Ice Harbor Dam2005 479 19 19 4.0 4 2006 289 26 27 9.0 9.3 2007 300 15 16 5.0 5.3 2008 687 27 29 3.9 4.2 2009 737 32 37 4.3 5 2010 1,611 76 78 4.7 4.8 2011 1,070 45 46 4.2 4.3 2012 842 48 51 5.7 6.1 2013 483 30 31 6.2 6.4 2014 687 16 16 2.3 2.3

Lower Granite Dam2005 469 33 36 7 7.7 2006 269 22 26 8.2 9.7 2007 285 22 26 7.7 9.1 2008 674 85 96 12.6 14.2 2009 711 69 76 9.7 10.7 2010 1,543 114 125 7.4 8.1 2011 1,013 153 180 15.1 17.8 2012 794 115 126 14.5 15.9 2013 427 39 45 9.1 10.5 2014 644 81 93 12.6 14.4

45

Figure 11. Fallback numbers by dam of tagged fish from the Snake River spring/summer

run Chinook salmon ESU, 2005-2014. Figure 12. Percent fallback by dam for tagged fish from the Snake River spring/summer

run Chinook salmon ESU, 2005-2014.

0

5

10

15

20

25

30

Bonneville The Dalles McNary Ice Harbor Lower Granite

Fal

lbac

k (%

)

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

0

5

10

15

20

25

30

Bonneville The Dalles McNary Ice Harbor Lower Granite

Fal

lbac

k (n

)2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

46

Figure 13. Differences in percent fallback between transported and inriver migrant fish from the Snake River spring/summer run Chinook salmon ESU (early and late runs combined) from 2005 to 2014. Percent fallback of inriver-migrant fish was subtracted from that of transported fish. Abbreviations:

BON Bonneville Dam TDA The Dalles Dam MCN McNary Dam ICH Ice Harbor Dam LGR Lower Granite Dam

-6.0

-4.0

-2.0

0.0

2.0

4.0

6.0

8.02005 2006 2007 2008 2009 2010 2011 2012 2013 2014

Fal

lbac

k pr

obab

ility

for

tran

spor

ted

vs. i

nriv

er fi

sh (

%)

BON TDA MCN ICH LGR

47

UpperColumbiaRiverSpringRunChinookSalmon

Fallback rates for fish from the Upper Columbia River spring run Chinook salmon ESU varied by year and dam (Table 17; Figures 14 and 15). The highest rates of fallback occurred at Bonneville Dam, where the mean fallback rate was 9.8 (range 5.2-14.8) and fallback probability was 9% (range 5-13%). Fallback rates at McNary Dam were nearly as high, with a mean estimated fallback rate of 9.4 (range 6.3-14.4), and a fallback probability of 9% (range 6-14%). The lowest rates of fallback for fish from the Upper Columbia ESU occurred at The Dalles Dam, although data for estimates were available for only two years (2013-2014). At The Dalles, both mean estimated fallback rate and fallback probability were 1 (range 0.6-1.3). Across years, the highest observed fallback for fish from the Upper Columbia ESU occurred in 2008, when both the mean fallback rate and fallback percentage for all dams combined was 9. Conversely, the lowest mean fallback metrics were observed in 2013, when both fallback rate and fallback percentage were 3.9.

48

Table 17. Fallback metrics for upper Columbia River spring run Chinook salmon.

Upper Columbia River spring run Chinook salmon

Number of fish

passing Number of fish that

fell back Total number of

fallbacks Fallback percent Fallback rate

Bonneville Dam2005 813 41 42 5 5.2 2006 653 55 63 8.4 9.6 2007 95 12 12 12.6 12.6 2008 114 9 9 7.9 7.9 2009 128 17 19 13.3 14.8 2010 454 32 32 7 7 2011 324 27 29 8.3 9 2012 475 52 59 10.9 12.4 2013 253 15 16 5.9 6.3 2014 364 39 47 10.7 12.9

The Dalles Dam2013 237 3 3 1.3 1.3 2014 331 2 2 0.6 0.6

McNary Dam2005 687 45 46 6.6 6.7 2006 523 56 60 10.7 11.5 2007 80 8 8 10 10 2008 90 13 13 14.4 14.4 2009 104 11 11 10.6 10.6 2010 377 27 29 7.2 7.7 2011 254 17 17 6.7 6.7 2012 397 25 25 6.3 6.3 2013 219 19 19 8.7 8.7 2014 310 34 34 11 11

Priest Rapids Dam2005 575 4 4 0.7 0.7 2006 496 9 10 1.8 2 2007 79 1 1 1.3 1.3 2008 90 2 2 2.2 2.2 2009 102 1 1 1 1 2010 370 3 3 0.8 0.8 2011 252 3 4 1.2 1.6 2012 312 6 6 1.9 1.9 2013 219 3 3 1.4 1.4 2014 307 5 5 1.6 1.6

Rock Island Dam2005 489 31 31 6.3 6.3 2006 450 21 22 4.7 4.9 2007 74 4 4 5.4 5.4 2008 86 10 10 11.6 11.6 2009 96 3 3 3.1 3.1 2010 362 20 23 5.5 6.4 2011 222 11 12 5 5.4 2012 377 25 28 6.6 7.4 2013 205 4 4 2 2 2014 231 8 9 3.5 3.9

49

Figure 14. Rate of upper Columbia River ESU Chinook fallback, or number of fallback

events at each dam per unique fish passing, from 2005-2014. Figure 15. Percent of upper Columbia ESU Chinook that fell back from 2005-2014.

0

5

10

15

20

25

30

Bonneville The Dalles McNary Priest Rapids Rocky Island

Fal

lbac

k (n

)

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

0

5

10

15

20

25

30

Bonneville The Dalles McNary Priest Rapids Rocky Island

Fal

lbac

k (%

)

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014

50

Discussion Our analysis focused on differences in run timing, survival, and fallback among tagged fish from major population groups (MPGs) or individual populations within and between the Snake River spring/summer run and Upper Columbia spring run Chinook salmon ESUs. We found a continuous sequence of run timing across these groups. However, tag groups from the South Fork Salmon River MPG and from the Pahsimeroi (Upper Salmon River MPG) and Imnaha (Grande Ronde/Imnaha MPG) populations had distinctly later arrival timing at Bonneville Dam than tagged fish from other MPGs or from other populations within their respective MPGs. These late-migrant Snake River fish were exposed to the summer Zone 6 harvest period at much higher rates than other fish, with majorities of the population exposed in some years. These three tag groups also exhibited exceptionally low survival (61-67%) during the same 3 years when longer-than-average travel times through Zone 6 were observed. For tagged Snake River fish overall (excluding Tucannon River fish), survival through the hydrosystem from Bonneville to Lower Granite Dam averaged just under 80% but ranged 65-90%. Upper Columbia tag groups averaged similar survival from Bonneville to Rock Island Dam (mean near 80%), but exhibited a narrower range across years (74-85%). Fish of hatchery origin and those with a history of juvenile transportation had survival rates about 3 percentage points lower than those of wild fish and inriver migrants. A history of transportation also increased fallback rates in Snake River fish. Cumulative survival for both ESUs was largely determined within Zone 6. However, survival above this reach was below 95% in some years. Notably, the lowest survival in all reaches occurred in the extraordinarily warm year of 2015. Fallback rates ranged 5-13% at all dams, with the lowest rates of fallback at The Dalles and Ice Harbor, and the highest rates at Bonneville, McNary and Lower Granite Dam. A juvenile migration history that included transport increased the rate of fallback for tagged adults from the Snake River spring/summer run ESU. Across years, fallback rates for transported fish varied from half to double the average rates.

51

Further analysis will help to clarify the impact of high temperatures and flows on arrival date, travel time, fallback and survival. It is likely that high flow and spill rates increased fallback and travel time in some years, which probably lowered survival. Stressful temperatures in the record-setting year of 2015 also probably influenced survival of late migrants, although most of these populations transited the Columbia and Snake Rivers prior to the heat wave in July. Some fish probably experienced higher mortality above the locations we report here (Rock Island and Lower Granite Dam), where they likely confronted intolerable tributary temperatures. Nonetheless, understanding relative migration timing and survival through the hydrosystem over the past decade provides valuable information for harvest managers.

52

References Boggs, C. T., M. L. Keefer, C. A. Peery, T. C. Bjornn and L. C. Stuehrenberg (2004).

"Fallback, reascension, and adjusted fishway escapement estimates for adult Chinook salmon and steelhead at Columbia and Snake River dams." Transactions of the American Fisheries Society 133(4): 932-949.

Crozier, L. G., B. J. Burke, B. Sandford, G. Axel and B. L. Sanderson (2014). "Adult Snake River sockeye salmon passage and survival within and upstream of the FCRPS." Research Report for U.S. Army Corps of Engineers, Walla Walla District.

Crozier, L. G. and J. A. Hutchings (2014). "Plastic and evolutionary responses to climate change in fish." Evolutionary Applications 7(1): 68-87.

Ford, M. J., Ed. (2011). Status review update for Pacific salmon and steelhead listed under the Endangered Species Act: Pacific Northwest, U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-113.

Gustafson, R. G., R. S. Waples, J. M. Myers, L. A. Weitkamp, G. J. Bryant, O. W. Johnson and J. J. Hard (2007). "Pacific salmon extinctions: quantifying lost and remaining diversity." Conservation Biology 21(4): 1009-1020.

Keefer, M. L., C. C. Caudill, C. A. Peery and S. R. Lee (2008). "Transporting juvenile salmonids around dams impairs adult migration." Ecological Applications 18(8): 1888-1900.

Lady, J., P. Westhagen and J. R. Skalski (2001). Survival under Propotional Hazards (SURPH 2.1). Columbia Basin Research. Seattle, University of Washington.

Marvin, D. and Nighbor, J. 2009. PIT tag specification document. Report of the Pacific States Marine Fisheries Commission to the PIT Tag Steering Committee. Available at www.ptagis.org/resources/document-library/ptagis-program-documents (March 2016).

PTAGIS. (2015). "Columbia Basin PIT Tag Information System." Retrieved Nov 1, 2015.