Table S1.1: Hatcheries used in the analysis. Name Hatchery Name State / Provin ce Origin Code Ocean Region River Number of releases Release Years (first - last) Coleman Coleman National Fish Hatchery CA SFB SFB Sacramento 15 1981-1990 Nimbus Nimbus Fish Hatchery CA SFB SFB American 8 1983-1990 Feather Feathery River Fish Hatchery CA SFB SFB Feather 17 1978-1990 Irongate Iron Gate Fish Hatchery CA NCA NCA Klamath 21 1979-1990 Trinity Trinity River Hatchery CA NCA NCA Trinity 28 1978-1990 Chetco Elk River Hatchery OR SOR SOR Chetco 13 1978-1990 Elk Elk River Hatchery OR COR COR Elk 13 1978-1990 Salmon(OR) Salmon River Hatchery OR NOR NOR Salmon 12 1978-1990 Stayton Roaring River Fish Hatchery OR COL COL Willamette 13 1978-1990 Big Creek Big Creek Hatchery OR COL COL Lower Columbia 19 1978-1990 Spring Creek Spring Creek National Fish Hatchery WA COL COL Lower Columbia 10 1978-1990 Cowlitz Cowlitz Salmon Hatchery WA COL COL Lower Columbia 12 1978-1988 Abernathy Abernathy Fish Technology Center WA COL COL Lower Columbia 6 1978-1990 Bonneville Bonneville River Hatchery OR MCOL COL Middle Columbia 17 1978-1990 White Little White Salmon WA MCOL COL Middle 14 1978-1990
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Table S1.1: Hatcheries used in the analysis.
Name Hatchery Name
State / Provinc
e
Origin Code
Ocean Region River
Number of releases
Release Years (first - last)
Coleman Coleman National Fish Hatchery CA SFB SFB Sacramento 15 1981-1990Nimbus Nimbus Fish Hatchery CA SFB SFB American 8 1983-1990Feather Feathery River Fish Hatchery CA SFB SFB Feather 17 1978-1990Irongate Iron Gate Fish Hatchery CA NCA NCA Klamath 21 1979-1990Trinity Trinity River Hatchery CA NCA NCA Trinity 28 1978-1990Chetco Elk River Hatchery OR SOR SOR Chetco 13 1978-1990Elk Elk River Hatchery OR COR COR Elk 13 1978-1990Salmon(OR) Salmon River Hatchery OR NOR NOR Salmon 12 1978-1990Stayton Roaring River Fish Hatchery OR COL COL Willamette 13 1978-1990Big Creek Big Creek Hatchery OR COL COL Lower Columbia 19 1978-1990Spring Creek Spring Creek National Fish Hatchery WA COL COL Lower Columbia 10 1978-1990Cowlitz Cowlitz Salmon Hatchery WA COL COL Lower Columbia 12 1978-1988Abernathy Abernathy Fish Technology Center WA COL COL Lower Columbia 6 1978-1990Bonneville Bonneville River Hatchery OR MCOL COL Middle Columbia 17 1978-1990
White Salmon Little White Salmon National Fish Hatchery WA MCOL COL Middle Columbia 14 1978-1990
Turtle WA UPCOL COL Upper Columbia 6 1984-1990Lyons Lyons Ferry Fish Hatchery WA UPCOL COL Snake 12 1985-1990Priest Priest Rapids Hatchery WA UPCOL COL Upper Columbia 13 1978-1990Yakima WA UPCOL COL Upper Columbia 3 1988-1990Forks Forks Creek Hatchery WA WAC WAC Nemah 6 1983-1988Humptulips Humptulips Salmon Hatchery WA WAC WAC Humptulips 7 1983-1990Quinault Quinault National Fish Hatchery WA WAC WAC Quinault 9 1979-1990Salmon(WA) Quinault National Fish Hatchery WA WAC WAC Salmon 7 1979-1984Samish Samish Hatchery WA PUSO PUSO Samish 6 1980-1990Grovers Grovers Creek Salmon Hatchery WA PUSO PUSO Grovers 8 1982-1990Hoko Hoko River Hatchery WA PUSO PUSO Hoko 4 1986-1990Elwha Elwha Hatchery WA PUSO PUSO Elwha 11 1979-1986Soos Soos Creek Hatchery WA PUSO PUSO Soos 6 1979-1990
Issaquah Issaquah State Salmon Hatchery WA PUSO PUSO Issaquah 7 1979-1988HoodCanal George Adams Hatchery WA PUSO PUSO Purdy 9 1979-1990Chilliwack Chilliwack River Hatchery BC SGEO SGEO Chilliwack 9 1982-1990Chehalis Chehalis River Hatchery BC SGEO SGEO Chehalis 9 1983-1990Capilano Capilano River Hatchery BC SGEO SGEO Capilano 14 1978-1990Cowichan Cowichan River Hatchery BC SGEO SGEO Cowichan 9 1980-1990Nanaimo Nanaimo BC SGEO SGEO Nanaimo 6 1980-1990Big Qualicum Big Qualicum Hatchery BC SGEO SGEO Big Qualicum 13 1978-1990Puntledge Puntledge River Hatchery BC SGEO SGEO Puntledge 15 1978-1990Quinsam Quinsam River Hatchery BC SGEO SGEO Quinsam 13 1978-1990Nitinat Nitinat Hatchery BC SWVI SWVI Nitinat 10 1981-1990Robertson Robertson Creek Hatchery BC SWVI SWVI Robertson 13 1978-1990Conuma Conuma River Hatchery BC SWVI SWVI Conuma 11 1980-1990
Table S1.2: Age conventions for Chinook salmon used in this paper.Calendar Year (c) Calendar Month Model Month (m) Season (s) Model Season (a) Spawner Age (y)
JanuaryFebruaryMarchApril 1 Spring 1May 2June 3 Summer 2July 4August 5
Fall 3
2
September 6October 7November 8
Winter 4December 9
BY+3
January 10February 11March 12April 13 Spring 5May 14June 15 Summer 6July 16August 17
Fall 7
3
September 18October 19November 20
Winter 8December 21
BY+4
January 22February 23March 24April 25 Spring 9May 26June 27 Summer 10July 28August 29
Fall 11
4
September 30October 31November 32
Winter 12December 33
BY+5
January 34February 35March 36April 37 Spring 13May 38June 39 Summer 14July 40August 41
Fall 15
5
September 42October 43November 44
Winter 16December 45
BY+6
January 46February 47March 48April 49 Spring 17May 50June 51 Summer 18July 52August 53
Fall 19 6September 54October 55
Table S1.3: Matrix defining areas for river entry. Rows indicate region of origin. Columns indicate Ocean Location. Cells marked with an X show ocean locations that contribute to river entry each fall.
Ocean LocationMONT SFB MEND NCA SOR COR NOR COL WAC PUSO SGEO SWVI NWVI CBC NBC SSEAK NSEAK
Orig
in R
egio
n
SFB X X XNCA X X X XSOR X X X XCOR X X X XNOR X X XCOL X X XMCOL X X XUPCOL X X XWAC X X X X XPUSO X X X XSGEO X X X X XSWVI X X X X X
Table S1.4. Point estimates of the proportional composition of a single cohort leaving the ocean to spawn. These values represent the long term average estimated proportional contribution of age classes to spawning from a single cohort. They help link the unobserved spawners in the statistical model ( p in equation S2.14). Individual release groups will vary from these proportions as a function of fisheries and early survival. Such variation is evident in Fig. S1.8 which shows the estimated cohort proportions for nine example releases in the model.
Figure S1.1: Commercial troll Chinook salmon effort salmon by season from spring 1979 to winter 1995-96 (units: vessel days). Black cells indicate areas with no recorded effort (includes both zero actual effort). Note the logarithmic color scale.
Figure S1.2: Commercial treaty troll Chinook salmon effort salmon by season from spring 1979 to winter 1995-96 (units: deliveries). Black cells indicate areas with no recorded effort (includes both zero actual effort and seasons with no information). While some amount of treaty troll effort almost certainly occurred within the Strait of Juan de Fuca, we considered all treaty troll to occur in region WAC (Washington coast). Note the logarithmic color scale.
Figure S1.3: United States (excluding Alaska) recreational hook and line Chinook salmon effort by season from spring 1979 to winter 1995-96 (units: Angler-Days). Black cells indicate areas with no recorded effort (includes both zero actual effort and seasons with no information). Note the logarithmic color scale.
Figure S1.4: Canadian recreational hook and line Chinook salmon effort by season from spring 1979 to winter 1995-96 (units: Boat Trips). Black cells indicate areas with no recorded effort (includes both zero actual effort and seasons with no information). Note the logarithmic color scale.
Figure S1.5. Sampling fraction of catch for commercial troll (top) and recreational fisheries (bottom) used in the model. Most values were calculated by taking the median of reported sampling fraction for fish caught in a particular location and season from RMIS. Not all locations and regions reported catch of our focal Chinook salmon releases, however, so for times and locations with missing sampling fraction, we averaged over adjacent areas and seasons (+/- one location north or south, +/- two seasons) to interpolate seasons and locations with missing data.
Figure S1.6. Estimated vulnerability to each gear type (left panel: troll; right panel: recreational) as a function of ocean age. Posterior means are shown. Different colors correspond to vulnerability curves associated with different retention lengths (total length in inches). As most retention lengths are reported in inches, we retain these units. A table of retention lengths used in the model for each location, gear type and season is presented as an accompanying excel file.
Figure S1.7. Estimated process error by region and model age. Lines and shading show among release mean ± SD for estimated process error for northern fall Chinook stocks (a), Columbia river and northern Oregon releases (b), and southern release regions (c). X-axis identifies the season and associated model season number (Table S1.2)
Figure S1.8. Estimated proportion of cohort observed in freshwater. Each panel shows an example cohort from a different origin region with the estimated proportional contribution of individuals from each age to freshwater over the course of a life-cycle. Grey bars indicate long-term mean spawning proportions by age for the appropriate origin region and black bars indicate posterior mean estimate of proportions for the release hatchery and year designated in the title note that the realized spawning distribution for a single year may differ substantially from the long-term mean age-distribution.
Figure S1.9: Estimated total (top), troll (middle), and US recreational (bottom) fishing mortality (F) by season and ocean region including both commercial and recreational mortality. Posterior means shown. Black indicates zero fishing mortality.
Figure S1.10. Estimated time-varying catchabilities (log(q)) for the four gear groups used in the model for years 1979-1995. Posterior means for each gear group are shown.
