Prepared in cooperation with the California Department of Water Resources and 

Bureau of Reclamation

The Regional Salmon Outmigration Study—Survival 

and Migration Routing of Juvenile Chinook Salmon in 

the Sacramento-San Joaquin River Delta during the 

Winter of 2008–09

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2013–1142

The Regional Salmon Outmigration Study—Survival 

and Migration Routing of Juvenile Chinook Salmon in 

the Sacramento-San Joaquin River Delta during the 

Winter of 2008–09

By Jason G. Romine, Russell W. Perry, Scott J. Brewer, Noah S. Adams, Theresa L. Liedtke, Aaron R. 

Blake, and Jon R. Burau

Prepared in cooperation with the California Department of Water Resources and Bureau of Reclamation

Open-File Report 2013-1142

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

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Suggested citation:

Romine, J.G., Perry, R.W., Brewer, S.J., Adams, N.S., Liedtke, T.L., Blake, A.R., and Burau, J.R., 2013,

The Regional Salmon Outmigration Study—Survival and migration routing of juvenile Chinook salmon in 

the Sacramento-San Joaquin River Delta during the winter of 2008–09: U.S. Geological Survey OpenFile Report 2013-1142, 36 p.

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endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

Abstract ......................................................................................................................................................... 1

Introduction.................................................................................................................................................... 2

Methods......................................................................................................................................................... 4

Telemetry System...................................................................................................................................... 4

Fish Tagging and Release ......................................................................................................................... 7

Tag Life...................................................................................................................................................... 9

Model Development ................................................................................................................................... 9

Preparation of Telemetry Data................................................................................................................. 11

Parameter Estimation .............................................................................................................................. 12

Survival through the Delta........................................................................................................................ 13

Results......................................................................................................................................................... 15

Tag Life.................................................................................................................................................... 15

River Conditions and Migration Timing .................................................................................................... 17

Detection Probabilities ............................................................................................................................. 19

Route-Specific Survival through the Delta................................................................................................ 19

Migration Routing..................................................................................................................................... 25

Predation Events...................................................................................................................................... 26

Discussion ................................................................................................................................................... 28

Acknowledgments ....................................................................................................................................... 30

References Cited......................................................................................................................................... 30

Appendix A .................................................................................................................................................. 33

Appendix B .................................................................................................................................................. 34

Appendix C.................................................................................................................................................. 35

Appendix D.................................................................................................................................................. 36

Figures

Figure 1. Maps showing the Sacramento-San Joaquin River Delta, California, with shaded 

regions showing river reaches that constitute Chinook salmon survival through the Delta for four 

different migration routes...............................................................................................................................3

Figure 2. Map showing location of telemetry stations used to estimate survival and migration route 

probabilities within four major migration routes of the Sacramento-San Joaquin River Delta, California, 

during the winter of 2008–09 .........................................................................................................................6

Figure 3. Schematic of the mark-recapture model used to estimate survival (Shi), detection (Phi), 

and route entrainment (Ψhl) probabilities of juvenile late fall-run Chinook salmon migrating through

the Sacramento–San Joaquin River Delta, California, for releases made in winter of 2008–09 ................. 10

Figure 4. Tag life and travel time of fish released at Sacramento, California, and arriving at downstream 

stations ........................................................................................................................................................ 16

Figure 5. Tag life and travel times for fish released at the Ryde release site, Sacramento-San Joaquin 

River Delta, California, and arriving at downstream stations ....................................................................... 16

Figure 6. Tag life and travel times for fish released at Georgiana Slough release site, Sacramento-San 

Joaquin River Delta, California, and arriving at downstream stations.......................................................... 17

Figure 7. Graphs showing river discharge, water exports, and Delta Cross Channel discharge during 

the migration period of tagged juvenile Chinook salmon migrating through the Sacramento-San 

Joaquin River Delta, California, during winter of 2008–09 ........................................................................... 18
iv

Figure 8. Graphs showing river discharge, water exports, and Delta Cross Channel discharge 

during the migration period of tagged juvenile Chinook salmon migrating through the Sacramento-San 

Joaquin River Delta, California, during winter of 2008–09 ........................................................................... 19

Figure 9. Graphs showing probability of surviving migration through the Sacramento-San 

Joaquin River Delta (Sh), California, for each of four migration routes for tagged late-fall juvenile 

Chinook salmon migrating from the Sacramento River................................................................................ 22

Figure 10. Graph showing probability of surviving migration through the Sacramento-San 

Joaquin River Delta (Sh), California, for each of four migration routes for tagged late-fall 

juvenile Chinook salmon migrating from the Sacramento River................................................................... 23

Figure 11. Graph showing comparison of route-specific survival between the Sacramento River 

(A), Sutter Slough (B1), and Steamboat Slough (B2), California, for late fall-run Chinook salmon 

tagged and released in winter 2008–09....................................................................................................... 24

Figure 12. Histogram showing cumulative behavioral scores for the predator filter algorithm..................... 27

Tables

Table 1. Summary of release dates, locations, and sample size of acoustically tagged late fall-run 

Chinook salmon released into the Sacramento-San Joaquin River Delta, California, during the 

winter of 2008–09 ..........................................................................................................................................8

Table 2. Route-specific survival through the Sacramento–San Joaquin River Delta (Sh; h= Route A, B, C,

or D), California, and the probability of migrating through each route (Ψh; h= Route A, B, C, or D) for 

acoustically tagged fall-run juvenile Chinook salmon from 10 release groups during winter 2008–09......... 21

Table 3. Probability of migrating through each route (Ψh; h=Route A, B, C, or D) for acoustically 

tagged late fall-run juvenile Chinook salmon released in winter 2008–09 conditional on gate position 

when fish entered junction 2, Sacramento-San Joaquin River Delta, California .......................................... 26

Table 4. Comparison of total survival estimates for truncated capture histories and non-truncated 

capture histories of Chinook salmon, Sacramento-San Joaquin River Delta, California.............................. 27
v

Conversion Factors and Datums

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

Flow rate

foot per second (ft/s) 0.3048 meter per second (m/s)

cubic foot per second (ft3/s) 0.02832 cubic meter per second 

(m3/s)

SI to Inch/Pound

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch (in.)

kilometer (km) 0.6214 Mile (mi)

Volume

liter (L) 33.82 ounce, fluid (fl. oz)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:°F=(1.8×°C)+32.

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L).

Datums

Horizontal coordinate information is referenced to North American Datum of 1983 (NAD 83).
vi

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1

The Regional Salmon Outmigration Study—Survival 

and Migration Routing of Juvenile Chinook Salmon in 

the Sacramento-San Joaquin River Delta during the 

Winter of 2008–09

By Jason G. Romine, Russell W. Perry, Scott J. Brewer, Noah S. Adams, Theresa L. Liedtke, Aaron R. 

Blake, and Jon R. Burau 

Abstract

Juvenile Chinook salmon (Oncorhynchus tshawytscha) emigrating from natal tributaries 

of the Sacramento River may use a number of migration routes to navigate the Sacramento-San 

Joaquin River Delta (hereafter called “the Delta”), each of which may influence their probability 

of surviving. We applied a mark-recapture model to data from acoustically tagged juvenile late

fall-run Chinook salmon that migrated through the Delta during the winter of 2008–09 to 

estimate route entrainment, survival, and migration times through the Delta. 

A tag-life study was conducted to determine the potential for premature tag failure. Tag 

failure began after 12days and continued until the 45th day. Travel times of tagged fish exceeded 

minimum tag-failure times, indicating that survival estimates obtained from this study were

negatively biased due to tag failure prior to fish exiting the Delta. Survival estimates were not 

adjusted and represent the joint probability of tag survival and fish survival. However, relative 

comparisons of survival among Chinook salmon choosing different routes appeared to be robust 

to tag failure, and migration-routing parameters were unaffected by tag failure.

Migration-routing patterns were consistent among release groups. The Sacramento River 

was the primary migration route for all release groups except one. The percentage of fish 

entering the Sacramento River ranged from 33 to 55 percent. Sutter and Steamboat Sloughs were 

the secondary migration route for 9 of the 10 releases. The percentage of fish migrating through 

this route ranged from 10 to 35 percent. Entrainment into the interior Delta ranged from 15 to 33 

percent. The Delta Cross Channel gates were open for 7 of the 10 releases. Entrainment into the 

interior Delta through the cross channel ranged from 1 to 27 percent.

We estimated route-specific survival for 10 release groups that were released between 

November 14, 2008, and January 19, 2009. Population-level survival through the Delta (SDelta) 

ranged from 0.019 (standard error of 0.012) to 0.277 (standard error of 0.041) among releases, 

which represent the probability of a fish surviving from Sacramento to Chipps Island with an 

operational transmitter. Sacramento River flows throughout the study period were approximately 

8,000–15,000 cubic feet per second at Freeport, suggesting that variability in flow contributed 

little to differences in survival between releases. Fish migrating through the Sacramento River 

had the highest survival for most releases. Survival in Sutter and Steamboat Sloughs was slightly

lower than survival in the Sacramento River for 7 of the 10 releases, but higher than survival in 

the Sacramento River for 3 releases. Survival in the interior Delta was lowest for all release 
2

groups except for one release in November. With the exception of this November release, 

survival patterns across release groups were similar to those of previous studies.

Introduction 

Many stocks of Chinook salmon (Oncorhynchus tshawytscha) in California, Washington, 

and Oregon are listed as threatened or endangered under the Endangered Species Act (Nehlsen 

and others, 1991; Myers and others, 1998). In the Central Valley of California, the winter, 

spring, and fall-late fall runs of Chinook salmon are federally listed as endangered, threatened, 

and “species of concern,” respectively (National Marine Fisheries Service, 1997). Recently, 

owing to below-target returns of fall Chinook salmon to the Sacramento River, the National 

Marine Fisheries Service declared a Federal Disaster and closed the 2008 salmon fishery along 

the West Coast (National Oceanic and Atmospheric Administration, 2008). Understanding 

factors affecting survival of salmon is critical to developing effective recovery strategies for 

these populations.

An important stage in the life history of Chinook salmon is the period of migration from 

natal tributaries to the ocean, when mortality of juvenile salmon in the Sacramento River may 

increase as a result of various anthropogenic and natural factors (Baker and Morhardt, 2001; 

Brandes and McLain, 2001; Williams, 2006). Juvenile Chinook salmon emigrating from the 

Sacramento River must pass through the Sacramento-San Joaquin River Delta (hereafter called

“the Delta”, fig. 1), a complex network of natural and man-made river channels linking the 

Sacramento River with San Francisco Bay (Nichols and others, 1986). Juvenile salmon may 

migrate through a number of routes on their journey to the ocean—for example, they may 

migrate within the main stem Sacramento River leading directly into San Francisco Bay (see 

Route A in fig. 1). However, juvenile salmon also may migrate through longer secondary routes 

such as the interior Delta, the network of channels to the south of the main stem Sacramento 

River (see Routes C and D in fig. 1). Juvenile salmon entering the interior Delta also are exposed 

to entrainment at water pumping projects in the southern Delta, which may decrease survival of 

fish using this migratory pathway (Kjelson and others, 1981; Brandes and McLain, 2001; 

Newman and Rice, 2002; Newman, 2003; Kimmerer, 2008; Newman, 2008; Newman and 

Brandes, 2010; Perry and others, 2010, 2012a). 

There is limited understanding of how water management actions in the Delta affect the 

population distribution and the route-specific survival of juvenile salmon during their 

outmigration. To address these uncertainties, we developed a mark-recapture model similar to 

that of Perry and others (2010) to estimate the route-specific components of population-level 

survival for acoustically tagged, late fall-run Chinook smolts migrating through the Delta. This 

study provided the first quantitative estimates of route-specific survival through the Delta, and of 

the fraction of the population that uses each migration route. Furthermore, we explicitly 

quantified the relative contribution of each migration route to population-level survival. As with 

other authors (Newman and Brandes, 2010), we found that survival of fish migrating through the 

interior Delta was lower than survival of fish migrating through the Sacramento River. The 

proportion of the population entering the interior Delta differed between releases, which can 

influence population-level survival by shifting a fraction of the population from a low-survival 

migration route (the interior Delta) to a high-survival route (the Sacramento River). However, 

differences in population-level survival between releases were caused by changes in survival for 

given migration routes. These findings indicated that variation in population-level survival was 

driven by variation in movement among routes and survival within routes.
3

Figure 1. Maps showing the Sacramento-San Joaquin River Delta, California, with shaded regions showing 

river reaches that constitute Chinook salmon survival through the Delta for four different migration routes. 

For routes C and D, the interior Delta is the large shaded region in the southernmost part of the migration 

route. Base map provided by Bureau of Reclamation, Mid-Pacific Region, MPGIS Service Center, 

Sacramento, CA.
4

This report is the result of efforts by California Department of Water Resources and the 

Bureau of Reclamation to resume analysis of data collected during the 2008 Regional Salmon 

Outmigration Study. For the complete scope of the Regional Salmon Outmigration study, see the 

independent review of the study plan (Calfed Bay-Delta Program, 2012). The 2008 study was 

affected by a complete stop-work order in early 2009 because of the fiscal crisis in California. 

The analysis of survival that we present is only one aspect of the much larger and more 

ambitious study plan. Because survival was not the only factor driving the study design (e.g., 2-d 

behavior at river junctions), last-minute decisions made prior to implementation of the field work 

negatively impacted our ability to obtain unbiased estimates of survival. Early in the planning 

process, we anticipated that a 30-d tag life was necessary to estimate survival without bias,

which could be achieved by manipulating the parameters (code length and period) of the signal 

emitted by the tag to extend its functional battery life. However, after compiling and reviewing 

tag-life data from recently completed studies in the Columbia River that had used the same tag, 

we determined that it was impossible to obtain a 30-d tag life. We considered using a relatively 

new tag that could meet our tag-life requirements, but it had not been used in large quantities,

and we were concerned that early-run production issues might affect the reliability of the new 

tag. At the time of this decision, the outmigration season was nearly upon us so we moved 

forward with the existing tag knowing that tag life would be about one-half (14–18 d) of what we 

thought was needed to meet the survival objectives. In anticipation of reduced tag life, we added 

additional releases of tagged fish at Ryde and Georgiana Slough, which are located about 

halfway through the study area. In theory, this would effectively achieve the 30-d tag life by 

using Sacramento-released fish to estimate survival to Ryde and Georgiana Slough, and then 

using the fish released at Ryde and Georgiana Slough to estimate survival to Chipps Island. Even 

with these contingencies in place, longer than anticipated travel times exceeded tag life. The 

decision was made to proceed with the study despite the uncertainty of meeting the survival 

objectives because other objectives of the larger study plan could be met. Specifically, we were 

able to gather previously unattainable information about route selection, migration behavior, and 

travel time, and detailed information on the behavior of fish at critical junctions (Delta Cross 

Channel and Georgiana Slough) in the Delta. This information is critical for developing 

strategies to manage water conveyance in the Delta, while contributing to the recovery of 

threatened and endangered salmon populations.

Methods

Telemetry System

Telemetry stations were deployed to monitor the movement of tagged fish among four 

major migration routes through the Delta (fig. 1)—the main stem Sacramento River (Route A), 

Steamboat and Sutter Sloughs (Route B), the interior Delta through the Delta Cross Channel 

(Route C), and the interior Delta through Georgiana Slough (Route D; fig. 1). Telemetry stations 

were labeled hierarchically to reflect the branching nature of channels at river junctions and their 

subsequent downstream convergence at the confluence of river channels (fig. 2). Each telemetry 

station consisted of a single node or multiple nodes (Hydroacoustic Technology Incorporated 

(HTI), Seattle, Washington) that identified individual fish based on pulse rate from a transmitter

or tag. Because the Sacramento River is the primary migration route, the ith telemetry station 

within this route was denoted as Ai from the release site to the last telemetry station in the Delta 
5

at Chipps Island (A5). Sutter and Steamboat Sloughs (labeled Bi) diverge from the Sacramento 

River at the first river junction and converge again with the Sacramento River upstream of A4.

Dual telemetry arrays were deployed at the entrances to Sutter and Steamboat Sloughs to 

quantify survival and movement within this region. The dual arrays allowed independent 

estimation of detection probabilities at these locations. The entrance to Sutter Slough was labeled 

B11 and the entrance to Steamboat Slough was labeled B21 (fig. 2). The interior Delta consisted of 

Routes C and D. The entrance to the interior Delta through Georgiana Slough was labeled as D1. 

Data from telemetry stations in the lower Mokelumne River and lower Potato Slough were 

pooled to form D2. The entrance to the interior Delta through the Delta Cross Channel was 

labeled as C1 where it diverges from the Sacramento River at the second river junction. Data 

from telemetry stations at the heads of the North and South Forks of the Mokelumne River were 

pooled to form station C2. Following this hierarchy, routes A, B, C, and D contained 4, 3, 2, and 

2 telemetry stations, respectively. We used a total of 12 telemetry stations to estimate survival. 

Parameter subscripting and coding of detection histories followed this hierarchical structure (see 

section, “Model Development”).
6

Figure 2. Map showing location of telemetry stations used to estimate survival and migration route 

probabilities within four major migration routes of the Sacramento-San Joaquin River Delta, California, 

during the winter of 2008–09. Red-filled circles labeled as hi show the location of telemetry station i with 

route h (h = A, B, C, or D). The Sacramento (Tower Bridge) release site was 40 river kilometers upstream

of station A2. The Georgiana and Ryde release sites are noted as the green-filled circles labeled as RGeo

and RRyd, respectively. Base map provided by Bureau of Reclamation, Mid-Pacific Region, MPGIS Service 

Center, Sacramento, CA.
7

Fish Tagging and Release

Juvenile late fall-run Chinook salmon were obtained from the Coleman National Fish 

Hatchery (about 340 river kilometers upstream of the Tower Bridge near Sacramento). Fish were 

surgically implanted with a 1.6-g tag with a 12-d expected battery life (HTI, Model 795-E). 

Between November 14, 2008, and January 19, 2009, 10 releases were made across

3 separate sites (table 1). For each release group, fish were released at Sacramento (Tower 

Bridge), Ryde, and Georgiana Slough (fig. 2, table 1). Multiple release sites were used because 

of the 12-d battery life of the transmitters. For the Sacramento release site, transmitters were 

expected to stop transmitting before fish from the uppermost release site exited the Delta at 

Chipps Island. Therefore, the two downstream release sites (i.e., Ryde and Georgiana Slough)

were used in an effort to obtain unbiased survival estimates in the lower regions of the Delta. 

Releases were made approximately every 2–3 d during this time period. For each release, fish 

were released first at Sacramento, and then released 1–2 d later at the downstream release 

locations, Ryde and Georgiana Slough. This was done to accommodate travel times of fish from 

the upper Sacramento to the lower release sites.

Untagged fish were transported from the hatchery to release sites where transmitters were 

implanted. Except for a minimum size criteria of 29.5 g, fish were randomly selected for tagging, 

resulting in a mean fork length (FL) of 149.9 mm (standard deviation =7.24) and mean weight of 

38.4 g (SD=6.00). Tag burden ranged from 0.022 to 0.054 and averaged 0.042 (SD=0.006). Fish 

were collected 21 times from November 9, 2008, to January 17, 2009, and were transported in 

265-L insulated tanks at a density of no greater than 20 g of fish per L of water. Water in 

transport tanks was maintained at 80–130 percent oxygen saturation using bottled oxygen. At 

each tagging site (Sacramento, Ryde, and Georgiana Slough), transport tanks were supplied with 

circulated fresh river water for 18–36 h prior to tagging. Fish were considered suitable for 

tagging if they were free of major injuries, had no external signs of gas bubble trauma, were less 

than 20-percent descaled, and had no other abnormalities.

To implant the transmitters, fish were anesthetized using buffered tricane®

methanosulfate (MS-222) at a dosage of between 70 and 90 mg/L. After a fish lost equilibrium, it 

was removed from the anesthetic bucket, placed in a bin containing river water and Stress Coat®

(Aquarium Pharmaceuticals, Inc.), weighed to the nearest 0.1 g, and measured to the nearest 

millimeter (FL). After a fish was anesthetized, a small incision was made in the abdomen 

between the pectoral fins and the pelvic girdle. The transmitter was inserted in to the peritoneal 

cavity, and the incision was closed with two interrupted sutures (4-0 nylon sutures with FS-2 

cutting needle). Immediately following the tagging procedure, each fish was placed in a 19-L 

recovery bucket filled with 7–10 L of fresh river water and supplied with bottled oxygen (at 

120–150 percent dissolved oxygen saturation) for at least 10 minutes. Each recovery bucket held 

a maximum of four surgically tagged, late fall-run Chinook salmon. After a minimum of 

10 minutes, buckets were poured into 121-L plastic drums that mostly were submerged in the 

river. These drums were perforated to allow water circulation and were placed inside a polyvinyl 

chloride frame for flotation to ensure fish had access to the water surface. 
8

Table 1. Summary of release dates, locations, and sample size of acoustically tagged late fall-run

Chinook salmon released into the Sacramento-San Joaquin River Delta, California, during the 

winter of 2008–09.

Release Date Release No. Release Location Sample Size

November 14-15, 2008 1 Sacramento 164

November 16-17, 2008 1 Ryde (Sacramento) 69

November 16-17, 2008 1 Georgiana Slough 101

November 17-18, 2008 2 Sacramento 179

November 19-20, 2008 2 Ryde (Sacramento) 69

November 19-20, 2008 2 Georgiana Slough 103

November 30- December 1 2008 3 Sacramento 177

December 2-3, 2008 3 Ryde (Sacramento) 61

December 2-3, 2008 3 Georgiana Slough 95

December 3-4, 2008 4 Sacramento 182

December 5-6, 2008 4 Ryde (Sacramento) 77

December 5-6, 2008 4 Georgiana Slough 137

December 14-15, 2008 5 Sacramento 191

December 16-17, 2008 5 Ryde (Sacramento) 69

December 16-17, 2008 5 Georgiana Slough 108

December 17-18, 2008 6 Sacramento 179

December 19-20, 2008 6 Ryde (Sacramento) 69

December 19-20, 2008 6 Georgiana Slough 108

December 30-31, 2008 7 Sacramento 175

January 1-2, 2009 7 Ryde (Sacramento) 69

January 1-2, 2009 7 Georgiana Slough 108

January 2-3, 2009 8 Sacramento 177

January 4-5, 2009 8 Ryde (Sacramento) 69

January 4-5, 2009 8 Georgiana Slough 109

January 13-14, 2009 9 Sacramento 177

January 14-16, 2009 9 Ryde (Sacramento) 69

January 15-16, 2009 9 Georgiana Slough 107

January 16-17, 2009 10 Sacramento 178

January 17-18, 2009 10 Ryde (Sacramento) 69

January 18-19, 2009 10 Georgiana Slough 106
9

Tag Life 

A tag-life study was conducted to estimate the battery-life distribution and to determine if 

survival estimates could be negatively biased due to tag failure prior to fish exiting the system. 

The study was conducted at the U. S. Geological Survey Columbia River Research Laboratory

(CRRL). Tags used in the tag-life study were identical to those implanted in fish. A total of 148 

795-E tags (HTI) were activated and placed in a circular 5-ft diameter tank with constantly 

flowing water. Tags emitted a constant double-pulse every 3–10 s with a pulse width of 1ms

depending on tag programming. Tags were monitored with two model 290 HTI hydrophones to 

determine when tags ceased operating.

Water temperature was controlled to match the daily mean (1999–2008) water 

temperature in the Sacramento River at the Rio Vista (RIV) gaging station (California 

Department of Water Resources, 2013). Tank water temperature was monitored using a digital 

thermometer and recorded every 30 minutes by two Onset® tidbit® data loggers. 

Tag-life time was calculated as the elapsed time between tag activation and the time of 

last detection recorded by the hydrophones. A Kaplan-Meier tag-life curve then was fitted to the 

data using the R statistical package (R Development Core Team, 2011). Cumulative travel time 

distributions for each release location and reach then were plotted against the tag-life curve. This 

allowed us to assess whether tagged fish exited the study area before tags began failing.

Model Development

We used a survival model similar to the model presented in Perry and Skalski (2010). In 

this model, we estimated detection (Phi), survival (Shi), and route entrainment probabilities (Ψhl). 

Detection probabilities (Phi) estimate the probability of detecting a transmitter assuming a fish is 

alive and the transmitter operational at telemetry station i within route h (h=A, B, C, D; fig. 2). 

Survival probabilities (Shi) estimate the probability of surviving from telemetry station i to i+1 

within route h (that is, to the next downstream telemetry station), conditional on surviving to 

station i (figs. 2 and 3). Route entrainment probabilities (Ψhl) estimate the probability of a fish 

entering route h at junction l (l=1, 2), conditional on fish migrating through junction l (figs. 2

and 3).

Dual telemetry stations within Sutter and Steamboat Sloughs downstream of each 

entrance allowed us to estimate route entrainment probabilities separately for each slough 

(figs. 2 and 3). The parameter ΨB11 estimates the probability of being entrained into Sutter 

Slough at station B11, and ΨB21 estimates the probability of being entrained into Steamboat 

Slough at station B21. Because route entrainment probabilities must sum to one at a given river 

junction, 1-ΨB11-ΨB21 = ΨA1 is the probability of remaining in the Sacramento River at the first 

junction (figs. 2 and 3). The second junction was modeled as a three-branch junction where ΨA2,

ΨC2, and 1-ΨA2-ΨC2 = ΨD2 estimate the probabilities of remaining in the Sacramento River 

(Route A), being entrained into the Delta Cross Channel (Route C), and entering Georgiana 

Slough (Route D) at junction 2 (figs. 2 and 3). The Delta Cross Channel gates were opened at 

about 8:45 a.m. and closed at 3:45 p.m. daily from November 14 to December 22, 2008, after 

which they were closed for the remainder of the study. Fish released during this time period 

passed the junction when gates were both open and closed. After the December 22, 2008 closure 

of the gates, they were not opened for the remainder of the study period; thus, fish released after 

this date could not enter the Delta Cross Channel. Therefore, we incorporated a parameter to 

estimate the probability of fish passing this river junction when the gates were open (ωopen,
10

fig. 3). We then estimated route entrainment probabilities conditional on gate position (i.e., 

Ψhl,open and Ψhl,closed). Route-specific survival was estimated for each release group. For the first 

seven release groups, route-specific survival represents the average survival during conditions 

experienced by each release-group; that is, with the Delta Cross Channel gates both open and 

closed. Route-specific survival for subsequent release groups represents survival when the gates 

were closed.

Figure 3. Schematic of the mark-recapture model used to estimate survival (Shi), detection (Phi), and route

entrainment (Ψhl) probabilities of juvenile late fall-run Chinook salmon migrating through the Sacramento–

San Joaquin River Delta, California, for releases made in winter of 2008–09. The parameter ωn is the 

probability of passing the second river junction when the Delta Cross Channel was either open or closed. 

Release sites are denoted by Rm (m = Sac, Ryde, and Geo), parameters subscripted by n are conditional 

on the position of the Delta Cross Channel gate, and m denotes parameters that can be estimated 

separately for each release site. Locations with two parallel horizontal bars represent a dual array.
11

Preparation of Telemetry Data

Given the scope of the telemetry array used in this study, manual marking of data files 

was not feasible. Therefore, we developed an alternative automated method for processing 

telemetry data. When performing echo selection on data from previous studies, we relied on a 

combination of automated processing and manual verification that required reviewing and handediting each detection. This approach required an amount of staff time directly proportional to 

the number of acoustic tag detections contained in a dataset. For this study, we processed a 

representative subsample of data files to estimate the number of total detections. Based on this 

estimate, it was predicted that as many as 20 person years of staff time could be required to 

manually verify every detection in the full dataset. As a result, the CRRL and the California 

Water Science Center (CWSC) collaborated in the development of an automated detection 

algorithm that could perform echo selection on the dataset with sufficient accuracy that the 

manual verification of each detection would not be required. To meet this goal, echo selection 

was performed on a benchmark dataset and the results were evaluated for accuracy after each

step in the algorithm development process and after each revision. The end result of this process 

was a package of software tools known as “fishCount.” This package then was used to automate 

echo selection for the entire data-set. Based on validation tests performed using a subset of the 

data, the accuracy of the automated echo selection performed using fishCount was estimated as 

follows:

1. The echo selection is estimated to have a false positive rate of 0.3 percent (3 out of 

every 1,000 detections are false)

2. The echo selection is estimated to have a true detection probability of 99.5 percent (5 

true detections are missed for every 1,000 detections found)

Although fishCount succeeds at extracting most true detections and eliminating most 

false detections, some false positives remain in the dataset, requiring application of a second 

level of processing. Given the probabilistic nature of the fishCount algorithm, false positives 

were more likely to occur at the beginning and end of detection histories for each fish. fishCount 

outputs detection events for each hour that a fish is detected at a telemetry node. Detection 

events span up to 1 h, but may be shorter if the tag is no longer detected at the telemetry node. 

For example, a detection history for a tag that was detected from 1:00 p.m. to 3:00 p.m. would be 

composed of two detection events, one spanning the 1p.m. hour and a second spanning the 

2 p.m. hour. For each detection event, fishCount produces a score, with higher values reflecting a 

higher likelihood that a given detection event was produced by a valid transmitter. This score 

variable was used as part of several criteria to eliminate false positives. False positives were 

defined as follows: detection events occurring prior to the fish being released, detection events 

with a score of less than 1, detection events with a score of less than 10 and fewer than 400 

pulses, detection events occurring later than 45 days after release, and detection events with a 

score of less than 5 and occurring 21 days after a previous detection event. These criteria were 

based on logical examination of the data. Tags detected prior to deployment could not be valid 

detections, and tags detected 45 days after deployment likely were false positives given that 100 

percent of the tags in the tag-life study expired after 45 days. Score values and pulse counts of 

these types of detection events were evaluated to develop the aforementioned criteria. 

Furthermore, detection events that were impossible, owing to unrealistic fish movement rates
12

between telemetry locations (e.g., 300 ft/s) also were examined in a similar way to derive criteria 

for removal of false positives. 

In addition to false positives, data were analyzed for potential predation events. Predation 

is an inherent problem in telemetry-based juvenile salmonid survival studies, where consumed 

smolts are not easily distinguished from live smolts. Only one method has been proposed for 

addressing this issue. Vogel (2010) proposed a three-pronged approach to evaluating the state of 

tags (smolt or consumed smolt) moving through a telemetry array. This approach was unrealistic 

for this study given the large number of tags and telemetry stations. Therefore, we developed 

criteria for assessing and classifying tags as smolt or predator as they moved through the array

based on behaviors of tagged predators reported in Vogel (2010, 2011).

Residence times and directional movement of the tag relative to direction of river flow 

were used to determine fish that possibly had been consumed by a predator. Each type of 

movement behavior was scored as 0 for smolt-like or 1 for predator-like behavior. Directional 

movement was one classification criterion. Dual arrays in several locations (B11, B21, and 

junction 2) allowed fine-scale determination of directional movements of tags in the system in 

relation to flow direction. Tags that showed continued upstream movement against the flow were 

flagged as potential predators (1). Additionally, fish that exceeded the 95th percentile of 

residence time at each telemetry station were flagged as demonstrating non-migratory or 

predator-like behavior. The 95th percentile of residence time was calculated from the entire 

population of residence times at each telemetry station owing to the consistent flows throughout 

the study. For each detection event, behavior that did not violate any of the aforementioned 

criteria was classified as 0 or smolt-like. A cumulative score for each fish then was tallied by 

summing the score for each behavior, with higher scores indicating a higher likelihood of 

predation. Fish with total behavioral scores greater than the 95th percentile of the score 

distribution were classified as predators. These transmitters were considered smolts up to the 

point at which their cumulative individual scores exceeded the 95th percentile score, after which 

they were identified as predators. Detection histories then were truncated at this point and used to 

create capture histories that were used for model parameter estimation. Survival models also 

were fit to non-truncated detection histories to examine the effect of predator removal on overall 

survival estimates. To verify this methodology, two-dimensional tracks at junction 2 were 

examined for predator- or smolt-like movement patterns. Junction 2 was populated with 30 nodes 

at the Delta Cross Channel gates, 16 at the Georgiana Slough and Sacramento River junction, 

and 16 at the Walnut Grove Bridge. This array of nodes allowed two-dimensional tracking of 

tags as they moved through the area. Movement patterns were examined for all fish moving 

through this area. Fish showing “looping” or “patrolling” type behaviors were classified as 

predator-like. After classifications were made, these determinations were compared to 

determinations made using the residence time and directional movement criteria.

Parameter Estimation

Detection histories describe concisely the migration and detection process of fish moving 

through the network of telemetry stations. For example, a fish with the history A0D0DA

indicates that it was released at Sacramento (“A”) and was not detected in the Sacramento River 

at A2 (“0”). It subsequently was detected at the head of Georgiana Slough (“D0”), at the end of 

Mokelumne/Potato Slough (“D”), and at Chipps Island (“A”). Each detection history represents 

one cell of a multinomial distribution where the probability of each cell is defined as a function 

of the detection, survival, and route entrainment probabilities (see Perry and others, 2010, for an 
13

example). Given these cell probabilities, the maximum likelihood estimates are determined by 

maximizing the likelihood function of a multinomial distribution with respect to the parameters:

( ) 1

, jkm

J n

km km jkm jkm

j

L Rn β π=∝∏  , (1)

where

Lkm is the likelihood for the kth release group (k = 1, ..., 10) at the mth release site 

(m=Sacramento (Sac), Georgiana Slough (Geo), Ryde (Ryd)),

Rkm is the number of fish released for each release group and release site,

njkm is the number of fish with the jth detection history in the kth release group at the 

mth release site, and

πjkm is the probability of the jth detection history in the kth release group at the mth 

release site expressed as a function of the parameters (β).

The likelihood was numerically maximized with respect to the parameters using algorithms 

provided in the software program USER (Lady and others, 2008; see appendix D). Parameters 

were estimated separately for each release (k) but simultaneously for all three release sites by 

expressing the joint likelihood as the product of Lk,Sac , Lk,Geo , and Lk,Ryd. The variancecovariance matrix was estimated as the inverse of the Hessian matrix. We used the delta method 

(Seber, 1982) to estimate the variance of parameters that are functions of the maximum 

likelihood estimates. Uncertainty in parameter estimates is presented as standard errors.

For each release, the full model was considered as the model with the fewest parameter 

constraints, which still allowed all parameters to be uniquely estimated. When parameter 

estimates occur at the boundaries of one (or zero), they cannot be estimated through iterative 

maximum likelihood techniques and must be set to one (or zero). In our study, many detection 

probabilities were set to one because all fish passing a given location were known to have been 

detected at that location. In some cases, survival probabilities were fixed at one because all fish 

detected at a given telemetry station also were detected at the next downstream location. 

Additionally, parameters for Route C (the Delta Cross Channel) were set to zero when the Delta 

Cross Channel was closed. A full detailing of parameter constraints applied under the full model 

is provided in appendixes A, B, and C.

The purpose of using three release areas was to reduce bias caused by potential tag 

failure. The Sacramento release groups likely would experience tag failure before arrival at 

Chipps Island; therefore, we used release groups at Ryde and Georgiana Slough to obtain 

unbiased survival estimates for the lower reaches of the Delta. Given tag failure rates, estimates 

in the lower reaches of the Delta for the Sacramento releases likely would be much lower than 

the estimates for fish released lower in the system at Ryde and Georgiana Slough. Our goal was 

to combine survival estimates from the multiple releases to minimize negative bias caused by tag 

failure.

Survival through the Delta

Survival through the Delta is defined as the probability of survival from the entrance to 

the Delta at station A2 to the exit of the Delta at station A5 (Chipps Island). Population-level 

survival through the Delta was estimated from the individual components as:

D

Delta

A

h h

h

S S == Ψ ∑ , (2)
14

where

Sh is the probability of surviving the Delta given the specific migration route 

taken through the Delta, and

Ψh is the probability of migrating through the Delta using one of four migration 

routes (A = Sacramento River, B = Steamboat and Sutter Sloughs, C = Delta 

Cross Channel, D = Georgiana Slough). 

Thus, population survival through the Delta is a weighted average of the route-specific survival 

probabilities with weights equal to the fraction of fish migrating through each route.

Migration route probabilities are a function of the route entrainment probabilities at each 

of the two river junctions: 

ΨA = ΨA1ΨA2, (3)

ΨB = ΨB11 + ΨB21, (4)

ΨC = ΨA1ΨC2, and (5)

ΨD = ΨA1ΨD2. (6)

For instance, consider a fish that migrates through the Delta using the Delta Cross 

Channel (Route C). To enter the Delta Cross Channel, this fish first remains in the Sacramento 

River at junction 1 with probability ΨA1, after which it enters the Delta Cross Channel at the 

second river junction with probability ΨC2. Thus, the probability of a fish migrating through the 

Delta through the Delta Cross Channel (ΨC) is the product of these route entrainment 

probabilities, ΨA1ΨC2.

Survival through the Delta for a given migration route (Sh) is the product of the reachspecific survival probabilities that trace each migration path through the Delta between the points 

A2 and A5 (Perry and others, 2010). However, to minimize bias resulting from tag failure, we 

combined reach-specific survival from different release groups to estimate route-specific 

survival. Reach-specific survival for the Sacramento release group was used through sites A4, B2, 

and D2 (fig. 2). The Ryde release group was used to estimate survival through the final reach of 

the Sacramento River (SA4r), and the Georgiana Slough release group was used to estimate 

survival through the final reach of the interior Delta (SD2g).

Survival through the Delta for fish that remain in the Sacramento River through the first 

and second river junctions is expressed as:

SA = SA1SA2SA3SA4r. (7)

Survival through the Delta for fish taking the Delta Cross Channel (Route C) and 

Georgiana Slough (Route D) is expressed similarly:

SC = SA1SA2SC1SC2SD2g, and (8)

SD = SA1SA2SD1SD2g. (9)

We combined Sutter and Steamboat Sloughs into a single migration route, but survival 

through the Delta can be estimated separately for fish that enter Sutter Slough and fish that enter 

Steamboat Slough:

SB = ΨB11SB1 + ΨB21SB2, (10)
15

where

SB is survival through the Delta for fish that enter either Sutter or Steamboat 

Sloughs,

SB1 and SB2are survival through the Delta for fish that enter Sutter and Steamboat 

Sloughs, respectively, and

SB1 and SB2are estimated as:

SB1 = SA1SB11SA4r , and (11)

SB2 = SA1SB21SA4r. (12)

We estimated route-specific survival and migration routing separately for each of 10

release groups, and represent season-wide estimates using a weighted mean and standard error. 

To estimate mean survival and routing, each release-specific parameter was weighted by CV-2

(CV is coefficient of variation) following methods described by Burnham and others (1987).

Results

Tag Life 

From October 28, 2008, through December 8, 2008, water temperature in the holding 

tank matched the 10-year daily mean water temperatures (1999–2008) in the Sacramento River 

at the RIV gaging station. Starting on December 9, 2008, tank temperature was matched to the 

daily mean at Rio Vista. Temperature in the tank started at 13.6°C, and was 10.9°C when the 

study ended. It should be noted that temperatures decreased suddenly on three occasions: a boiler 

malfunction caused temperatures to decrease to 6.3°C for 61 hours, a power outage caused 

temperatures to decrease to 8°C for 4 hours, and a pump malfunction caused temperatures to 

decrease to 3.1°C for 79 hours. Such decreases in temperature are expected to reduce actual tag 

life, thereby making our estimates more conservative than would normally be expected in the 

Sacramento River during this time of year. 

The average life of the 795-E tags was 22.4 d (figs. 4, 5, and 6). Three tags expired after 

12 d and the last tag expired after 45.3 d. For fish released at the Sacramento site, approximately 

90–98 percent of detected tags were still operational upon fish arrival at downstream locations 

(figs. 4 and 5). For fish released at the two lower locations, only 85–90 percent of the tags were 

operational upon arriving at downstream telemetry stations (figs. 5 and 6). This suggests that our 

survival estimates represent the joint probability of tag survival and fish survival rather than fish 

survival only. As such, survival estimates presented are negatively biased. 
16

Figure 4. Tag life and travel time of fish released at Sacramento, California, and arriving at downstream 

stations. The dashed line represents tag-life survival distribution function. Other lines represent the 

cumulative distribution of arrival time to each telemetry station.

Figure 5. Tag life and travel times for fish released at the Ryde release site, Sacramento-San Joaquin 

River Delta, California, and arriving at downstream stations. The dashed line represents tag-life survival 

distribution function. Other lines represent the cumulative distribution of arrival time to each telemetry 

station.
17

Figure 6. Tag life and travel times for fish released at Georgiana Slough release site, Sacramento-San 

Joaquin River Delta, California, and arriving at downstream stations. The dashed line represents tag-life 

survival distribution function. Other lines represent the cumulative distribution of arrival time to each 

telemetry station.

River Conditions and Migration Timing

River conditions remained fairly constant throughout the study period. Discharge in the 

Sacramento River at Freeport was approximately 10,000 ft3

/s during all releases (fig. 7). A spike 

in flow occurred at the end of December 2008 and the end of January 2009 (fig. 7). Median 

travel times for fish released at the Sacramento release site to the second junction (Stations A3, 

C1, and D1 in fig. 2) were fairly consistent throughout the study (range=2.78 d for R7, and 5.29 d 

for R4). Releases 4, 5, and 8 had the greatest variability in travel times, with some fish taking 

more than 15 d to reach the junction. Fish from R7 took the shortest amount of time to reach the 

junction, with 75 percent of the fish arriving at the junction in approximately 4 d. The increase in 

discharge to about 15,000 ft3

/s just prior to the release of these fish may have contributed to their

faster travel times (fig. 7). Fish from R4 took the longest amount of time to reach the junction. 

After 12 d, only 75 percent of the fish had reached the junction. Release 4 was associated with 

the lowest flows during the study period.

For fish released at Ryde and Georgiana Slough, median travel time to Chipps Island 

ranged from 3.16 d for R1 to 8.91 d for R9 (fig. 8). All other groups had median travel times of 

7–8 d to Chipps Island. Between-group travel times for the downstream release groups were less 

variable than for the Sacramento releases. In general, 90 percent of the fish released at the 

downstream locations arrived at Chipps Island about 12–14 d after release (fig. 8).
18

Figure 7. Graphs showing river discharge, water exports, and Delta Cross Channel discharge during the 

migration period of tagged juvenile Chinook salmon migrating through the Sacramento-San Joaquin River 

Delta, California, during winter of 2008–09. Boxplots show the distribution of arrival dates at Junction 2 on 

the Sacramento River by fish released at Sacramento. The symbols R1-R10 are plotted at the release dates. 

Whiskers represent the 10th and 90th percentiles, the box encompasses the 25th to 75th percentiles, and 

the line bisecting the box is the median arrival date. River discharge (solid line) is average daily discharge 

of the Sacramento River at Freeport (near telemetry station A2), Delta Cross Channel discharge (dotted 

line) is the daily average discharge, and water exports (dashed line) are the total daily discharge of water 

exported from the Delta at the pumping projects.
19

Figure 8. Graphs showing river discharge, water exports, and Delta Cross Channel discharge during the 

migration period of tagged juvenile Chinook salmon migrating through the Sacramento-San Joaquin River 

Delta, California, during winter of 2008–09. Boxplots show the distribution of arrival dates at Chipps Island 

(A5) of fish released at Ryde and Georgiana Slough. The symbols R1-R10 are plotted at the release dates. 

Whiskers represent the 10th and 90th percentiles, the box encompasses the 25th to 75th percentiles, and 

the line bisecting the box is the median arrival date. River discharge (solid line) is average daily discharge 

of the Sacramento River at Freeport (near telemetry station A2), Delta Cross Channel discharge (dotted 

line) is the daily average discharge, and water exports (dashed line) are the total daily discharge of water 

exported from the Delta at the pumping projects.

Detection Probabilities

For all release groups, detection probabilities at many telemetry stations were high (see 

appendix A; table A1). Detection probabilities ranged from 0.5 (PD2,Sac , R1 ) to 1.00 for many 

locations and release groups throughout the study. For each location, detection probabilities 

remained fairly constant for all release groups. Overall, detection probabilities for the first two 

release groups were the lowest. The dual arrays (PB11, PB21, PA5) had detection probabilities 

greater than 0.90 with the exception of PA5, Ryd and PA5,Sac for R1 and PA5,Geo for R2.

Route-Specific Survival through the Delta

Due to evidence of premature tag failure, route-specific and total survival through the 

Delta were calculated using survival estimates of fish released at Sacramento to A4 and D2 and 

estimates of survival for Ryde and Georgiana Slough release groups to Chipps Island (fig. 3). 

Total survival through the Delta (SDelta) ranged from 0.019 for R2 to 0.277 for R6 (table 2). The 

overall weighted mean for SDelta was 0.188 (standard error of 0.023). Survival was lowest for the 

four groups released from November 14, 2008, to December 6, 2008. These releases occurred 

during decreasing flows in the Delta. Release 6 had the highest estimated survival
20

(SDelta = 0.277). This release occurred during one of the peak discharge events between 

December 14 and 20, 2008. However, travel times by other release groups were shorter. Travel 

time for all other releases did not appear to have a direct affect on survival. Release 7 had the 

shortest travel times, but survival for this release group was only 0.108 (table 2) and only slightly 

above the median overall survival estimate. 

Route-specific survival was variable between release groups. Fish remaining in the 

Sacramento River (Route A) had the highest survival for 6 of the 10 releases (table 2; figs. 9 and 

10). Fish migrating through the interior Delta (Routes C and D) has the lowest survival for all 

releases with the exception of R2 (Route C, fig. 9). This estimate was driven by a single fish that 

migrated through Route C for this release. Fish migrating through Route B had the highest 

survival for releases R8, R9, and R10 (fig. 10) followed by Route A.

Survival patterns within Route B (Sutter and Steamboat Sloughs) were consistent 

between release groups. Survival generally was higher for Steamboat Slough (SB2) than for Sutter 

Slough (SB1; table 2; fig. 11), with the exception of R8. Survival for Steamboat Slough was 

similar to survival estimates for Sacramento River for all release groups. 

Percentages of fish migrating through the interior Delta influenced the overall survival 

through the Delta. Overall survival decreased as percentages of fish entering the interior Delta 

increased because survival through the interior Delta was consistently lower than for other 

migration routes (figs. 9 and 10).
21

Table 2. Route-specific survival through the Sacramento–San Joaquin River Delta (Sh; h= Route A, B, C, or D), California, and the probability of 

migrating through each route (Ψh; h= Route A, B, C, or D) for acoustically tagged fall-run juvenile Chinook salmon from 10 release groups during 

winter 2008–09. 

[Population survival through the Delta (SDelta) is the average of route-specific survival weighted by the probability of migrating through each route. Values in 

parentheses represent standard error. Overall mean is the weighted average of release-specific estimates, with weights equal to the inverse relative variance 

squared. The Delta Cross Channel gates were closed for releases 8, 9, and 10. Mean values of the routing probabilities are not constrained to sum to 1]

Release SA SB SC SD ΨΑ ΨΒ ΨC ΨD SDelta

1 0.135(0.039) 0.051(0.035) 0.000(NA) 0.058(0.048) 0.560(0.055) 0.106(0.030) 0.046(0.022) 0.288(0.050) 0.098(0.027)

2 0.012(0.012) 0.008(0.009) 0.119(0.088) 0.052(0.041) 0.495(0.051) 0.322(0.046) 0.011(0.011) 0.172(0.039) 0.019(0.012)

3 0.038(0.019) 0.025(0.014) 0.019(0.019) 0.004(0.004) 0.333(0.055) 0.349(0.049) 0.275(0.052) 0.043(0.024) 0.027(0.012)

4 0.119(0.036) 0.100(0.033) 0.071(0.038) 0.066(0.029) 0.457(0.054) 0.263(0.043) 0.072(0.028) 0.208(0.046) 0.100(0.025)

5 0.262(0.048) 0.208(0.043) 0.120(0.091) 0.195(0.056) 0.511(0.041) 0.288(0.036) 0.014(0.010) 0.187(0.032) 0.232(0.037)

6 0.306(0.050) 0.290(0.053) 0.162(0.074) 0.179(0.042) 0.500(0.043) 0.318(0.039) 0.023(0.013) 0.159(0.032) 0.277(0.041)

7 0.126(0.031) 0.087(0.026) 0.000(NA) 0.088(0.026) 0.547(0.046) 0.228(0.037) 0.009(0.009) 0.215(0.039) 0.108(0.023)

8 0.233(0.040) 0.259(0.047) NA 0.121(0.033) 0.539(0.046) 0.305(0.040) NA 0.155(0.034) 0.223(0.035)

9 0.199(0.036) 0.236(0.046) NA 0.094(0.029) 0.507(0.048) 0.259(0.040) NA 0.234(0.041) 0.184(0.029)

10 0.099(0.029) 0.120(0.036) NA 0.093(0.033) 0.516(0.050) 0.265(0.041) NA 0.219(0.043) 0.103(0.024)

Overall 

mean 0.211 (0.025) 0.210(0.025) 0.099(0.024) 0.127(0.016) 0.512(0.014) 0.288(0.270) 0.184(0.064) 0.207(0.188) 0.188(0.023)
22

Figure 9. Graphs showing probability of surviving migration through the Sacramento-San Joaquin River 

Delta (Sh), California, for each of four migration routes for tagged late-fall juvenile Chinook salmon 

migrating from the Sacramento River. The width of each bar shows the fraction of fish migrating through 

each route (Ψh), and the total area under the bars yields SDelta. Labels A–D represent the Sacramento 

River, Steamboat and Sutter Sloughs, the Delta Cross Channel, and Georgiana Slough, respectively. 

Panels are labeled by release groups (R1 – R6).
23

Figure 10. Graph showing probability of surviving migration through the Sacramento-San Joaquin River 

Delta (Sh), California, for each of four migration routes for tagged late-fall juvenile Chinook salmon 

migrating from the Sacramento River. The width of each bar shows the fraction of fish migrating through 

each route (Ψh), and the total area under the bars yields SDelta. Labels A–D represent the Sacramento 

River, Steamboat and Sutter Sloughs, the Delta Cross Channel, and Georgiana Slough, respectively. 

Panels are labeled by release groups (R7 – R10). The Delta Cross Channel gates were closed for all fish 

encountering the junction in releases R8, R9, and R10.
24

Figure 11. Graph showing comparison of route-specific survival between the Sacramento River (A), Sutter 

Slough (B1), and Steamboat Slough (B2), California, for late fall-run Chinook salmon tagged and released in 

winter 2008–09.
25

Migration Routing

Migration routing at the first junction, (Sutter Slough, Steamboat Slough, and Sacramento 

River) was consistent between release groups (appendix B, table B1). Estimates of ΨA1 ranged 

from 0.651 to 0.894, indicating that most fish remained in the Sacramento River. Of the fish 

entering Sutter and Steamboat Sloughs, most migrated through Sutter Slough, Route B1 

(appendix B, table B1). 

Migration routing at the second junction depended on the status of the Delta Cross 

Channel gates when fish migrated through the junction. The gates were open only for releases 1–

7 (table 3). These release groups entered the junction when the gates were both open and closed

during the migration period of each release group. The probability of fish encountering the gates 

when they were open (ωopen) ranged from 0.012 (R7) to 0.911 (R3). Of the fish that entered the 

junction when the gates were open, entrainment into the Delta Cross Channel ranged from 13.6

to 66.7 percent (with the exception of R7, for which entrainment was 100 percent owing to a 

single fish passing the junction when the gate was open; appendix B, table B1). On average,

47percent of the fish that entered the junction when the gates were open were entrained into the 

Delta Cross Channel. 

Migration route probabilities account for the joint probability of route entrainment at both 

river junctions and indicate the fraction of the population using each migration route. We 

observed that with the cross channel gate closed, the fraction of fish remaining in the Sacramento 

River was higher (ΨA,Closed) for all release groups than when the gate was open (ΨA,open; table 3).

Additionally, migration route probabilities for Georgiana Slough (ΨD) were higher with the gates 

closed than with the gates open. These results indicate that operation of the Delta Cross Channel 

entrains fish that otherwise would have remained in the Sacramento River or entered Georgiana 

Slough. For fish passing the Delta Cross Channel when it was open, the overall probability of 

migrating to the interior Delta through the Delta Cross Channel ranged from 0.00 to 0.186

(table 3).

Aggregating over open and closed gate operations for each release group, the Sacramento 

River was the primary migration route taken by all releases except for R3, with 33–56 percent of 

fish migrating through this route (Route A; table 2). Sutter and Steamboat Sloughs (Route B)

ranked second for all releases except for R1, where a higher proportion of fish entered Georgiana

Slough (table 2; fig. 9), and R3, where the greatest percentage of fish migrated through Route B. 

Because most release groups experienced both open and closed gate conditions, a relatively 

small fraction of fish entered the Delta Cross Channel (Route C). For all but one release, less 

than 10 percent of each release group entered the Delta Cross Channel. Entrainment into 

Georgiana Slough (Route D) ranged from 4.3 to 28.8 percent among release groups (table 2).
26

Table 3. Probability of migrating through each route (Ψh; h=Route A, B, C, or D) for acoustically tagged late 

fall-run juvenile Chinook salmon released in winter 2008–09 conditional on gate position when fish entered 

junction 2, Sacramento-San Joaquin River Delta, California. 

[Values in parentheses represent standard error. Migration routing probabilities for Route B are the same for both

gate positions]

Release ΨΑ,Open ΨΒ,Open/closed ΨC,Open ΨD,Open ΨΑ,Closed ΨD,Closed ωopen

1 0.298(0.172) 0.106(0.030) 0.596(0.173) 0(0) 0.582(0.056) 0.312(0.054) 0.077(0.030)

2 0.339(0.171) 0.322(0.046) 0.170(0.147) 0.170(0.147) 0.506(0.051) 0.172(0.04) 0.063(0.031)

3 0.317(0.056) 0.349(0.049) 0.302(0.056) 0.032(0.022) 0.488(0.146) 0.163(0.141) 0.911(0.042)

4 0.451(0.062) 0.263(0.043) 0.100(0.039) 0.186(0.052) 0.473(0.095) 0.265(0.092) 0.720(0.060)

5 0.285(0.157) 0.288(0.036) 0.280(0.156) 0.147(0.130) 0.522(0.042) 0.189(0.033) 0.049(0.021)

6 0.426(0.119) 0.318(0.039) 0.256(0.118) 0(0) 0.507(0.044) 0.175(0.034) 0.089(0.030)

7 0(0) 0.228(0.037) 0.772(0.037) 0(0) 0.554(0.046) 0.218(0.039) 0.012(0.012)

8 NA 0.305(0.040) NA NA 0.539(0.046) 0.155(0.034) NA

9 NA 0.259(0.040) NA NA 0.507(0.048) 0.234(0.041) NA

10 NA 0.265(0.041) NA NA 0.516(0.050) 0.219(0.043) NA

Predation Events

Our analyses classified 117 fish as showing predator like-behavior. The break point for 

smolt-like or predator-like behavior (i.e, the 95th percentile) was a total behavioral score of 66 

predator-like behaviors (fig. 12). The detection histories for these fish were truncated at the 

detection event at which the cumulative behavioral score was greater than 66. Examination of 2D 

tracks of tags passing through the Delta Cross Channel and the Georgiana Slough junction 

supported the classifications assigned by our approach. Overall, removal of predators had little 

effect on the estimate of SDelta. At most, the removal of predators decreased survival estimates by 

2 percentage points (table 4). This suggests our survival estimates at the scale of an entire 

migration route are robust to consumption of tagged smolts by predators. However, using a 

predator-detection algorithm to classify fish as predator-like is critical because reach-specific 

survival estimates are more likely to be biased by predators moving among reaches within the 

study area.
27

Figure 12. Histogram showing cumulative behavioral scores for the predator filter algorithm. The red 

vertical line (Cumulative Score = 66) represents the 95th percentile. The x and y axes are truncated for 

clarity.

Table 4. Comparison of total survival estimates for truncated capture histories and non-truncated capture 

histories of Chinook salmon, Sacramento-San Joaquin River Delta, California. 

[Values in parentheses represent the standard error. Overall mean is the weighted mean]

Release SDelta predators removed SDelta predators not removed

1 0.098 (0.027) 0.104 (0.029)

2 0.019 (0.012) 0.021 (0.013)

3 0.027 (0.012) 0.034 (0.016)

4 0.100 (0.025) 0.109 (0.027)

5 0.232 (0.037) 0.244 (0.039)

6 0.277 (0.041) 0.277 (0.041)

7 0.108 (0.023) 0.112 (0.024)

8 0.223 (0.035) 0.236 (0.036)

9 0.184 (0.029) 0.208 (0.031)

10 0.103 (0.024) 0.121 (0.028)

Mean 0.188 (0.023) 0.199 (0.023)
28

Discussion

Because of slow travel times coupled with short tag life, survival estimates from this 

study were low when compared to previous survival estimates of juvenile Chinook salmon in the 

Delta. As such, these estimates are negatively biased by tag failure. Caution should be exercised 

when interpreting these estimates on an absolute basis because they represent the probability of 

both the fish surviving and the tag remaining operational. In contrast, differences in survival 

among routes were similar to previous years, with the Sacramento River representing a highsurvival route relative to the interior Delta. Therefore, while the absolute magnitude of survival 

is negatively biased, relative comparisons of survival between routes appear to remain robust to 

tag failure. Furthermore, migration routing parameters (Ψ) should remain unbiased in the 

presence of tag failure. 

Three lines of evidence indicate that tag failure was the primary cause of low survival 

estimates observed in this study. First, the tag-life study showed that tags began failing after only 

12 d, which is much less than travel times typically observed through the Delta (Perry and others,

2010). Second, our estimates were 25–50 percent lower than previous survival estimates in the 

Delta (Perry and others 2010, 2012a), which is consistent with the negative bias that would be 

expected, given the evidence of tag failure. For example, Perry and others (2012a) estimated 

SDelta ranging from 0.174 to 0.543 for the winters of 2006–07 to 2008–09. Third, for four of the 

release groups (R3, R4, R9, and R10), survival estimates were much lower than for tagged fish 

released in conjunction with a study conducted by the U.S. Fish and Wildlife Service (USFWS; 

Perry and Skalski, 2010). The fish in the USFWS study were tagged and released simultaneously 

with fish from this study. SDelta for R3 and R4 were 0.027 and 0.100, respectively, whereas SDelta

for USFWS fish released simultaneously with R3 and R4 was 0.386. Likewise, SDelta for R9 and 

R10 was 0.103 and 0.188, whereas survival of tagged fish from the USFWS study was 0.339 for 

fish released simultaneously with R9 and R10. The USFWS study used acoustic transmitters with 

a 70-d expected battery life; therefore, the survival estimates likely were unaffected by tag 

failure. These findings provide strong evidence of negative bias induced by tag failure.

In designing our study, we took steps to guard against modest tag failure, but higher-thanexpected tag failure combined with low flows and consequent long travel times offset these 

efforts to eliminate bias. The primary purpose of releasing fish at two sites further downstream in 

the Delta was to obtain survival estimates through the lower Delta that were unaffected by tag 

failure. We tagged fish at the release sites rather than at the hatchery because tagging fish at the 

hatchery would have used considerable battery life prior to release of fish. Despite these efforts, 

the cumulative travel time distributions for fish released from lower Delta sites revealed that 

transmitters began failing before all fish passed Chipps Island (figs. 5 and 6). Although our 

approach of combining survival estimates from different release sites reduced bias resulting from

tag failure, it could not eliminate the bias.

Inferences about migration routing remain unbiased in the presence of tag failure. As 

with other studies, the Sacramento River was the primary migration route used by tagged fish 

(Perry and others, 2010, 2012b). Sutter and Steamboat Sloughs had the second highest routing 

probability for most releases. Routing probabilities for Sutter and Steamboat Sloughs were 

higher than for the Sacramento River for the January releases. Perry and others (2012a) showed 

similar results.

Migration through the interior Delta was low for all releases. At most, the probability of 

being entrained into the interior Delta was 0.32 (R3). For this release group, a large fraction of 

fish encountered the Delta Cross Channel when the gates were open (ωopen =0.91) and were 
29

subsequently entrained into the Delta Cross Channel. The probability of migrating through Route 

C for this release was 0.28, whereas all other estimates for entrainment into the Delta Cross 

Channel were less than 0.08. The maximum entrainment probability observed by Perry and 

others (2012a) during migration years 2006–07 to 2008–09 for Route C was 0.23 (December 

2006). Aside from release 3, entrainment into the interior Delta occurred from Georgiana Slough. 

Entrainment into the interior Delta from Georgiana Slough ranged from 0.04 to 0.28, and was 

highest when flows were at their maximum during the study (R1).

Relative survival between migration routes was consistent with previously published 

works. Fish migrating through the Sacramento River had the highest probability of survival for 

most releases, relative to alternative routes. Survival estimates for Sutter and Steamboat Sloughs 

were higher than those for the Sacramento River for the January 2009 releases (R8, R9, R10). This 

is consistent with results presented by Perry and others (2012a). For one release group (R2),

survival for the interior Delta was more than 10 percentage points greater than survival in other 

routes (fig. 9). Furthermore, survival for all routes was extremely low for R2. For example, the 

survival rate for the Sacramento River was only 0.012, an order of magnitude less than the mean 

survival rate (0.211, table 2). Additionally, survival for Sutter and Steamboat Sloughs was less 

than 1 percent for this release group. For all other releases, survival was lowest for fish entering 

the interior Delta through the Delta Cross Channel.

Our predator determination methods classified approximately five percent of detected 

tags as exhibiting predator-like behavior within the acoustic array at some point in their 

migration. This agrees closely with previously published values. Perry and others (2012b) 

estimated observed predation rates of 6 percent during the 2009–10 migration year, and values 

typically range from 6 to 10 percent. Our method only allows for determination of tags that are 

detected within the array and does not account for other sources of mortality such as avian 

predators, entrainment into water export facilities, handling stress, or poor environmental 

conditions. Additionally, for a tag to be classified, it must have been detected within the array. A 

tag that was released and not detected may or may not have been consumed by a predator. 

Without detections of the tag, we could not classify the source of mortality. Furthermore, 

survival estimates from multi-state mark recapture approaches are estimates of the joint 

probability of tag and fish survival. The approach we used allows for adjustment in the breakpoint at which tags were classified as smolts or predators and is easily modified to meet the 

criteria of the user. The approach is based on objective criteria rather subjective determinations 

and allows for multiple survival estimates to be generated from different break-point values 

without excessive re-examination of the data. With 5 percent of detected fish classified as 

predators, survival estimates decreased approximately 1–2 percentage points. 

Given the results of this study, methodologies must be developed that address bias 

induced by tag failure. Statistical methods exist to correct survival estimates for tag failure 

(Cowen and Schwarz, 2005; Townsend and others, 2006), but our research indicates that these 

methods fail to completely remove the bias. These methods use the observed travel-time 

distribution to estimate the average probability of tag failure, which is then used to backcalculate true fish survival. However, in the presence of tag failure, the travel-time distribution 

also is negatively biased because fish with long travel times are not detected. Therefore, the 

estimate of the average probability of tag failure also is negatively biased, and the procedure will 

remove some but not all of the bias from the survival estimate (Holbrook and others, 2013). 
30

Acknowledgments

Our analysis would not have been possible without the extensive efforts of U.S. 

Geological Survey field staff and collaboration with staff of the U.S. Fish and Wildlife Service, 

the Coleman National Fish Hatchery, and the California Department of Water Resources.

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33

Appendix A

Table A1. Detection probability estimates, with standard error in parentheses, for all releases of acoustically tagged late-fall juvenile Chinook 

salmon, Sacramento-San Joaquin River Delta, California, winter 2008–09.

[Parameters not estimated are indicated by an “NA” in the estimate column, and parameters fixed at a constant value are noted by an “NA” in parentheses]

Parameter R1 R2 R3 R4 R5 R6 R7 R8 R9 R10

PA2 0.821 (0.043) 0.571 (0.062) 0.911 (0.042) 0.967 (0.023) 0.990(0.01) 1.000 (NA) 0.977 (0.016) 1.000 (NA) 0.961 (0.022) 0.776 (0.051)

PA3 0.961 (0.038) 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.984 (0.016) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PA4 0.933 (0.065) 1.000 (NA) 1.000 (NA) 0.857 (0.094) 0.962 (0.037) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PA4, Ryd 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.909 (0.087) 1.000 (0) 1.000 (NA) 1.000 (NA) 0.962 (0.038) 0.964(0.035) 1.000 (NA)

PA5,Geo 1.000 (NA) 0.667 (0.333) 1.000 (NA) 0.926 (0.08) 0.929 (0.074) 0.947 (0.054) 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.952 (0.054)

PA5,Ryd 0.889 (0.086) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.977 (0.024) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PA5,Sac 0.889 ( 0.074) 1.000 (NA) 1.000 (NA) 0.977 (0.025) 1.000 (NA) 0.974 (0.026) 1.000 (NA) 0.992 (0.009) 1.000 (NA) 1.000 (NA)

PB11 1.000 (NA) 0.988 (0.012) 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.964 (0) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PB2 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.9 (0.067) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PB21 1.000 (NA) 0.947 (0.053) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.995 (0.006)

PC1 0.857 (0.094) 1.000 (NA) 1.000 (NA) 0.857 (0.094) 0.961 (0.038) 1.000 (NA) 0 (0) NA NA NA

PC2 0.720 (0.234) 1.000 (NA) 0.750 (0.153) 1.000 (NA) 0.961 (0.038) 1.000 (NA) 1.000 (NA) NA NA NA

PD1 0.857 (0.094) 1.000 (NA) 1.000 (NA) 0.857 (0.094) 0.961 (0.038) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PD2,Sac 0.500 (0.353) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA)

PD2,Geo 1.000 (NA) 0.750 (0.217) 0.875 (0) 0.700 (0.145) 0.846 (0.1) 0.950 (0.049) 1.000 (NA) 1.000 (NA) 1.000 (NA) 0.900 (0.095)
34

Appendix B

Table B1. Routing probability estimates, with standard error in parentheses, for all releases (Ri ) of acoustically tagged late-fall juvenile Chinook 

salmon, Sacramento-San Joaquin River Delta, California, winter 2008–09. 

[Parameter: Open and closed signify the status of the Delta Cross Channel gates. Parameters not estimated are indicated by an “NA” in the estimate column, and 

parameters fixed at a constant value are noted by an “NA” in parentheses]

Parameter R1 R2 R3 R4 R5 R6 R7 R8 R9 R10

ΨA1 0.894 (0.030) 0.678 (0.046) 0.651 (0.049) 0.737 (0.043) 0.712 (0.036) 0.682 (0.039) 0.772 (0.037) 0.695 (0.040) 0.741 (0.040) 0.735 (0.041)

ΨA2,closed 0.651 (0.059) 0.746 (0.057) 0.750 (0.217) 0.641 (0.123) 0.734 (0.045) 0.744 (0.048) 0.718 (0.049) 0.776 (0.048) 0.684 (0.053) 0.701 (0.056)

ΨA2,open 0.333 (0.192) 0.500 (0.250) 0.488 (0.078) 0.611 (0.076) 0.400 (0.219) 0.625 (0.171) 0.000 (NA) NA NA NA

ΨB11 0.077 (0.026) 0.182 (0.037) 0.254 (0.045) 0.150 (0.035) 0.192 (0.032) 0.198 (0.034) 0.160 (0.032) 0.198 (0.035) 0.059 (0.021) 0.141 (0.032)

ΨB21 0.029 (0.016) 0.140 (0.034) 0.095 (0.030) 0.113 (0.031) 0.096 (0.024) 0.120 (0.027) 0.069 (0.022) 0.107 (0.027) 0.201 (0.037) 0.124 (0.030)

ΨC2,open 0.667 (0.192) 0.250 (0.217) 0.463 (0.078) 0.136 (0.052) 0.394 (0.218) 0.375 (0.171) 1.000 (NA) NA NA NA

ΨD2,closed 0.349 (0.059) 0.254 (0.057) 0.250 (0.217) 0.359 (0.123) 0.266 (0.045) 0.256 (0.048) 0.282 (0.049) 0.224 (0.048) 0.316 (0.053) 0.299 (0.056)

ΨD2,open 0.000 (NA) 0.250 (0.217) 0.049 (0.034) 0.253 (0.070) 0.206 (0.183) 0.000 (NA) 0.000 (NA) NA NA NA
35

Appendix C

Table C1. Survival probability estimates, with standard error in parentheses, for all releases (Ri ) of acoustically tagged late-fall juvenile 

Chinook salmon, Sacramento-San Joaquin River Delta, California, winter 2008–09. 

[Parameter: Open and closed signify the status of the Delta cross channel gates. Gates were closed for all fish in releases R8, R9, and R10.

Parameters not estimated are indicated by an “NA” in the estimate column, and parameters fixed at a constant value are noted by an “NA” in parentheses]

Parameter R1 R2 R3 R4 R5 R6 R7 R8 R9 R10

SA1 0.648 (0.040) 0.634 (0.041) 0.546 (0.039) 0.599 (0.037) 0.830 (0.027) 0.822 (0.029) 0.768 (0.032) 0.757 (0.033) 0.691 (0.035) 0.699 (0.039)

SA2 0.878 (0.049) 0.837 (0.056) 0.732 (0.059) 0.780 (0.052) 0.931 (0.025) 0.928 (0.026) 0.848 (0.036) 0.835 (0.039) 0.859 (0.038) 0.754 (0.052)

SA3,closed 0.506 (0.077) 0.477 (0.075) 0.333 (0.272) 0.884 (0.136) 0.865 (0.049) 0.902 (0.038) 0.869 (0.043) 0.780 (0.054) 0.635 (0.067) 0.617 (0.071)

SA3,open 1.000 (NA) 0.500 (0.354) 0.650 (0.107) 0.720 (0.107) 1.000 (NA) 0.800 (0.179) NA NA NA NA

SA3,Ryd 0.449 (0.060) 0.304 (0.055) 0.400 (0.061) 0.429 (0.066) 0.783 (0.050) 0.826 (0.046) 0.899 (0.036) 0.799 (0.053) 0.767 (0.054) 0.522 (0.06)

SA4,Sac 0.588 (0.122) 0.682 (0.099) 0.143 (0.094) 0.491 (0.103) 0.388 (0.062) 0.609 (0.068) 0.377 (0.067) 0.680 (0.070) 0.545 (0.087) 0.552 (0.092)

SA4,Ryd 0.435 (0.107) 0.048 (0.046) 0.154 (0.071) 0.333 (0.086) 0.389 (0.066) 0.449 (0.068) 0.226 (0.053) 0.472 (0.069) 0.529 (0.070) 0.306 (0.077)

SB11 0.125 (0.117) 0.198 (0.089) 0.208 (0.083) 0.438 (0.124) 0.567 (0.09) 0.815 (0.087) 0.476 (0.109) 0.769 (0.083) 0.571 (0.187) 0.353 (0.116)

SB21 0.333 (0.272) 0.387 (0.126) 0.556 (0.166) 0.583 (0.142) 0.800 (0.103) 0.738 (0.118) 0.556 (0.166) 0.643 (0.128) 0.667 (0.096) 0.799 (0.104)

SB3 0.562 (0.400) 0.200 (0.126) 0.500 (0.158) 0.438 (0.136) 0.517 (0.093) 0.577 (0.091) 0.267 (0.114) 0.522 (0.094) 0.750 (0.097) 0.500 (0.118)

SC1 1.000 (NA) 1.000 (NA) 0.842 (0.148) 1.000 (NA) 1.000 (NA) 1.000 (NA) 1.000 (NA) NA NA NA

SC2 0.000 (NA) 1.000 (NA) 0.500 (0.144) 0.500 (0.204) 0.500 (0.353) 0.667 (0.272) 0.000 (NA) NA NA NA

SD1,Sac,closed 0.764 (0.523) 0.400 (0.126) 1.000 (NA) 0.432 (0.220) 0.801 (0.080) 0.810 (0.086) 0.500 (0.102) 0.706 (0.111) 0.458 (0.102) 0.600 (0.11)

SD1,Geo 0.228 (0.042) 0.259 (0.081) 0.095(0.032) 0.261 (0.059) 0.416 (0.063) 0.614 (0.054) 0.574 (0.048) 0.541 (0.048) 0.458 (0.048) 0.335 (0.055)

SD1,Sac, open 1.000 (NA) 1.000 (NA) 0.000 (NA) 0.478 (0.162) 1.000 (NA) 0.000 (NA) 0.000 (NA) NA NA NA

SD2,Sac 0.113 (0.107) 0.125(0.117) 0.111 (0.105) 0.372 (0.149) 0.304 (0.096) 0.270 (0.104) 0.417 (0.142) 0.588 (0.144) 0.455 (0.150) 0.167 (0.108)

SD2,Geo 0.130 (0.070) 0.225 (0.164) 0.111 (0.106) 0.302 (0.100) 0.312 (0.083) 0.318 (0.064) 0.274 (0.057) 0.271 (0.058) 0.347 (0.068) 0.295 (0.085)

ωopen 0.077 (0.030) 0.063 (0.031) 0.911 (0.042) 0.720 (0.060) 0.049 (0.021) 0.089 (0.030) 0.012 (0.012) NA NA NA
36

Appendix D

Files of release-specific capture histories and model likelihoods for program USER were included as a separate attachment to this report.
For additional information contact:

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, Washington 98115

http://wfrc.usgs.gov/

Publishing support provided by the U.S. Geological Survey

Publishing Network, Tacoma Publishing Service Center
Romine and others— The Regional Salmon Outmigration Study—Survival and Migration Routing of Juvenile Chinook Salmon in the Sacramento-San Joaquin River 

Delta during the Winter of 2008–09—Open-File Report 2013–1142