Prepared in cooperation with Bureau of Reclamation

Detection Probability of an In-Stream Passive Integrated 

Transponder (PIT) Tag Detection System for Juvenile 

Salmonids in the Klamath River, Northern California, 2011

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012–1001
Cover: Photograph showing upstream view of one of the pass-by antennas at Klamath River 

kilometer 252.7, northern California, August 25, 2010. (Photograph taken by Brian Hayes, 

U.S. Geological Survey.)
Detection Probability of an In-Stream Passive Integrated 

Transponder (PIT) Tag Detection System for Juvenile 

Salmonids in the Klamath River, Northern California, 2011 

By John W. Beeman and Brian Hayes, U.S. Geological Survey; and Katrina Wright, U.S. Fish and Wildlife Service

Prepared in cooperation with the Bureau of Reclamation

Open-File Report 2012–1001

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2012

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Suggested citation:

Beeman, J.W., Hayes, B., and Wright, K., 2012, Detection probability of an in-stream passive integrated transponder 

(PIT) tag detection system for juvenile salmonids in the Klamath River, northern California, 2011: U.S. Geological 

Survey Open-File Report 2012-1001, 14 p.

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

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.................................................................................................................................................................... 1

Description of Study Area.............................................................................................................................................. 2

Methods......................................................................................................................................................................... 3

PIT Tag Detection System ......................................................................................................................................... 3

Radio-Telemetry Tag Detection System .................................................................................................................... 7

Tagging and Releasing Fish ...................................................................................................................................... 7

Data Analysis............................................................................................................................................................. 8

Detection Probabilities................................................................................................................................................... 9

Discussion ..................................................................................................................................................................... 9

Acknowledgments ........................................................................................................................................................11

References Cited..........................................................................................................................................................11

Appendix 1. Detections of PIT Tags from Other Studies. .............................................................................................13

Appendix 2. Capture Histories of PIT- and Radio-Tagged Yearling Coho Salmon from Iron Gate Hatchery Used to 

Evaluate a PIT Detection System in the Klamath River, 2011 ......................................................................................14

Figures

Figure 1. Map of the study area of the Klamath River in northern California................................................................. 2

Figure 2. Upstream view of one of the pass-by antennas at Klamath River kilometer 252.7, northern California, 

August 25, 2010 ............................................................................................................................................................ 3

Figure 3. Graph of the discharge downstream of Iron Gate Dam between the time of PIT tag detection system 

installation and the end of the study period, Klamath River, northern California............................................................ 4

Figure 4. Upstream views of the pass-through antennas on July 27 and June 1, 2011, Klamath River, 

northern California ......................................................................................................................................................... 5

Figure 5. Upstream view of the PIT detection system mounted in the frame net at Klamath River 

kilometer 271.2, northern California............................................................................................................................... 6
iv

Conversion Factors and Datum

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

SI to Inch/Pound 

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

Volume

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

liter (L) 2.113 pint (pt)

liter (L) 1.057 quart (qt)

liter (L) 0.2642 gallon (gal)

cubic meter (m3)

milligram per liter (mg/L)

264.2

0.00000058

gallon (gal) 

pounds per gallon (lb/gal)

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. 

Datum

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83). 
1 

Detection Probability of an In-Stream Passive Integrated 

Transponder (PIT) Tag Detection System for Juvenile 

Salmonids in the Klamath River, Northern California, 2011 

By John W. Beeman and Brian Hayes, U.S. Geological Survey; and Katrina Wright, U.S. Fish and Wildlife Service

Abstract 

A series of in-stream passive integrated transponder (PIT) detection antennas installed across the 

Klamath River in August 2010 were tested using tagged fish in the summer of 2011. Six pass-by 

antennas were constructed and anchored to the bottom of the Klamath River at a site between the Shasta 

and Scott Rivers. Two of the six antennas malfunctioned during the spring of 2011 and two passthrough antennas were installed near the opposite shoreline prior to system testing. The detection 

probability of the PIT tag detection system was evaluated using yearling coho salmon implanted with a 

PIT tag and a radio transmitter and then released into the Klamath River slightly downstream of Iron 

Gate Dam. Cormack-Jolly-Seber capture-recapture methods were used to estimate the detection 

probability of the PIT tag detection system based on detections of PIT tags there and detections of radio 

transmitters at radio-telemetry detection systems downstream. One of the 43 PIT- and radio-tagged fish 

released was detected by the PIT tag detection system and 23 were detected by the radio-telemetry 

detection systems. The estimated detection probability of the PIT tag detection system was 0.043 

(standard error 0.042). Eight PIT-tagged fish from other studies also were detected. Detections at the 

PIT tag detection system were at the two pass-through antennas and the pass-by antenna adjacent to 

them. Above average river discharge likely was a factor in the low detection probability of the PIT tag 

detection system. High discharges dislodged two power cables leaving 12 meters of the river width 

unsampled for PIT detections and resulted in water depths greater than the read distance of the antennas, 

which allowed fish to pass over much of the system with little chance of being detected. Improvements 

in detection probability may be expected under river discharge conditions where water depth over the 

antennas is within maximum read distance of the antennas. Improvements also may be expected if 

additional arrays of antennas are used. 

Introduction

Passive integrated transponder (PIT) tags commonly are used to study fish, including their 

movements and survival (Williams and others, 2001; Hewitt and others, 2010). PIT tags are radio 

frequency identification tags that transmit an alphanumeric code as they pass through the 

electromagnetic field emitted by a detection antenna (Prentice and others, 1990). PIT tags are useful for 

various purposes because many types are relatively small (slightly larger than a grain of rice) and are 

powered by a detection antenna and therefore have a nearly infinite life. However, PIT antennas emit a 
2 

weak electromagnetic field, therefore, the tags must be between about 10 and 100 cm from the antenna 

to be detected, depending on the tag and antenna system. PIT-tagged fish in the Klamath River are being 

used to study juvenile salmonid movements within and among several habitats and tributaries, but most 

of the antenna systems are located in small tributaries or backwaters where detection probabilities 

generally are high. PIT detection systems in the mainstem Klamath River would be useful for linking 

movements of fish tagged in the Klamath River or its tributaries as they move between habitats. The 

goal of this study was to evaluate the detection probability of an in-stream PIT antenna system in the

Klamath River. 

Description of Study Area

The study was conducted in the Klamath River in northern California between the Iron Gate Fish 

Hatchery and a site slightly upstream of the confluence of the Klamath and Scott Rivers (fig. 1). This 

section of the Klamath River was chosen for evaluating the PIT detection system because water depth in 

the main-stem river downstream may be too high for use of PIT systems due to tributary accretions, and 

there are studies using PIT tags in nearby tributaries, such as the Shasta River (Chris Adams, California 

Department of Fish and Game, written commun., November 16, 2011).

Figure 1. Map of the study area of the Klamath River in northern California.
3 

Methods

PIT Tag Detection System

The primary PIT detection system was a Digital Angel FS1001M multiplexing transceiver and 

six full-duplex PIT tag antennas at Klamath River kilometer 252.7 from the river mouth. Six 6.1 × 0.60 

m PIT tag antennas were constructed and installed in a pass-by orientation (mounted horizontally to the 

river bottom; Connolly and others, 2008) in late August 2010 when Iron Gate Dam discharge was near

the lowest of the year (fig. 2). These antennas spanned the width of the river when installed. Each 

antenna consisted of wires and electronics housed inside a 10.2-cm diameter polyvinyl chloride pipe and 

formed a rectangle. At the time of installation, river discharge near Iron Gate Dam was about 1,000 ft3

/s 

and gage height was 0.74 m (USGS gaging station 11516530). Water depth at the PIT array site ranged 

between 0.6 and 1.25 m during installation. The antennas were attached to the river bottom in a 1 × 6 

array perpendicular to flow to span as much of the 42.6 m wide river channel as possible (six antennas 

laid end-to-end across the river). Antenna 1 was located nearest the transceiver on river left (facing

downstream) and each subsequent antenna was installed extending out from the previous antenna 

towards the opposite bank. Each antenna was secured to the river bottom using about ten 10–20 cm 

earth anchors driven 1.5 m below the cobble substrate leaving a loop at the surface for attachment. 

Figure 2. Upstream view of one of the pass-by antennas at Klamath River

kilometer 252.7, northern California, August 25, 2010.
4 

Once installed, the PIT tag detection system was operated for several weeks for testing and 

evaluating before it was turned off for the winter. On March 9, 2011, the PIT transceiver and solar 

power were re-installed for more evaluation prior to release of the radio- and PIT-tagged study fish. 

During this testing period, data were downloaded periodically to examine antenna diagnostics. These 

downloads provided information that indicated two antennas farthest from the receiver were no longer 

functioning effectively, presumably due to high flows and debris disconnecting the power cable or 

dislodging an antenna in mid-April 2011 (fig. 3). High river discharge and water depth also prevented 

these two antennas from being repaired or replaced. Two additional 3 × 0.91 m antennas were installed 

in a pass-through (upright) orientation in a backwater area adjacent to the original PIT tag antennas to 

increase coverage during high river discharge (fig. 4; Zydlewski and others, 2006). Antennas were 

numbered 1–6 across the river beginning at river left shore near the receiver, thus antenna numbers 1 

and 2 were pass-through antennas and antennas 3–6 were pass-by antennas. The damage to the two 

original antennas farthest from the receiver resulted in approximately 12 m of the river width without 

PIT antennas. The revised PIT detection system, consisting of two pass-through and four pass-by 

antennas, was operational on June 1, 2011, and it functioned continuously until August 10, 2011. 

During the initial testing and throughout the intended study period, the antennas were 

consistently detecting test tags 35–41 cm off the antenna plane on the pass-by antennas. The two passthrough antennas were detecting tags throughout the 3 m × 0.91 m opening and up to 16 cm from the 

outside edges of the opening. Estimated depth at the PIT detection site when the first tagged fish were 

released from Iron Gate Hatchery was 1.5–1.8 m. Gage height was 1.5 m and river flow was about 

3,000 ft3

/s at USGS gaging station 11516530 downstream of Iron Gate Dam. River discharge at this 

gage between August 1 and August 10, 2011, averaged 1,948.1 ft3

/s and ranged from 904 to 5,620 ft3/s. 

Figure 3. Graph of the discharge downstream of Iron Gate Dam 

between the time of PIT tag detection system installation and the end of

the study period, Klamath River, northern California. Note the high 

discharge in April 2011 relative to the 50-year record.
5 

Figure 4. Upstream views of the pass-through antennas on July 27

(top photograph) and June 1, 2011 (bottom photograph), Klamath River, 

northern California. Average hourly discharges measured at USGS gaging 

station 11516530 downstream of Iron Gate Dam were 1,090 ft3/s on 

July 27 and 3,200 ft3/s on June 1, 2011. 
6 

A secondary PIT detection system deployed from a frame net was installed in a flat-water run 

habitat on the river right at Klamath River kilometer 271.2. A wide-mouthed net was anchored to a 23.1 

× 1.5 m metal frame. The wide opening faced upstream and a 15-m net tapered down to a Biomark 0.6 × 

0.6 m waterproof pass-through antenna at the downstream end (fig. 5). A Destron FS2001 transceiver on 

the right bank recorded tag detections and data were downloaded weekly. This PIT array was operated 

from June 2 to July 13, 2011, when decreasing water depth made the pass-through trap ineffective. 

 Figure 5. Upstream view of the PIT detection system mounted in the frame net

 at Klamath River kilometer 271.2, northern California. 
7 

Radio-Telemetry Tag Detection System

Detections of radio-telemetry tags were based on two independent systems. The systems were 

installed at Klamath River kilometer 234 upstream of the confluence of the Klamath and Scott Rivers. 

Each independent system consisted of a solar panel and voltage regulator, 12-volt battery, and a Lotek 

SRX-400 radio-telemetry receiver receiving radio signals from two 3-element and two 6-element Yagi 

antennas combined into a single input. The radio receivers sequentially scanned each of three radio 

frequencies (164.320, 164.480, and 166.478 MHz) for 8.7 s in a repeating loop. Both systems monitored 

the same spatial area and were similar in design and location to those used in the studies of juvenile 

coho salmon migration and survival in 2006–09 (Beeman and Juhnke, 2009). The systems operated 

continuously from a few days prior to the date of fish release to August 18, 2011, when the systems

were removed at the end of the study period. 

Tagging and Releasing Fish

Fish for this study were obtained from the Iron Gate Fish Hatchery located along the Klamath 

River at river kilometer 310. A total of 43 yearling coho salmon of hatchery origin surgically implanted 

with radio transmitters and PIT tags were released on June 1 and 2, 2011, 1 day after the tags were 

surgically implanted. Three additional hatchery coho salmon implanted with only PIT tags were 

released on June 2, 2011, 1 day after tags were surgically implanted. We used Lotek model NTC-M-2 

radio transmitters, which had dimensions of 13 × 5 × 3 mm in size, weighed 0.43 g in air and 0.29 g in 

water, and had a 16 cm trailing antenna. The expected life of this transmitter using a coded burst rate of 

7.8 s was 46 d, and 24 transmitters of the same specifications tested in 2009 had a mean life of 65.3 d 

(range 58.3–69.5 d; John Beeman, U.S. Geological Survey, unpublished data). We used DestronFearing SST full-duplex PIT tags, which had dimensions of 12.5 mm long × 2.1 mm diameter and 

weighed 0.10 g in air. PIT tags do not use a battery and so have an infinite life. The PIT tags operated at 

a frequency of 134.2 kHz. 

The size of each fish was recorded immediately prior to tagging. The mean weight of fish before 

tagging was 59.8 g [standard deviation (SD) = 23.3] and the mean fork length was 178 mm (SD = 24.7). 

The combined weight of the radio transmitter and PIT tag represented 0.89 percent of the mean body 

weight of the fish and ranged from 0.45 to 3.0 percent of each individual’s body weight. 

The procedure used to surgically implant the radio transmitters and PIT tags was similar to that 

used by Adams and others (1998) and previous Klamath River radio-telemetry studies (Stutzer and 

others, 2006; Beeman and others, 2008; Wright and others, 2011). Before surgery, each fish was 

anesthetized in a bath of tricaine methanesulfonate (70 mg/L Finquel MS-222, Argent Chemical 

Laboratories, Redmond, Washington) until loss of equilibrium occurred. A foam pad with a central 

groove shaped to fit the dorsal surface of a small fish was covered with a chamois soaked in PolyAqua 

(Novalek, Inc., Hayward, California) and used to support the fish’s body during surgery. Fish were 

placed ventral side up on the surgical support pad, and the gills were flushed with anesthetic solution 

(20 mg/L MS-222) for the duration of the surgery through tubing placed in fish’s mouth. The mean 

(± 1 SD) time to complete each surgical procedure was 4 min 02 s (± 26 s). Water temperatures in the 

hatchery tank, bait tank used to hold fish after surgery, and the Klamath River nearby ranged from 

9.98 to10.74 o

C and dissolved oxygen was 89.2 percent or greater during tagging, holding, and release. 
8 

Surgical tools and equipment were disinfected according to the procedures described by 

Summerfelt and Smith (1990). To reduce the likelihood of infection, PIT tags and radio transmitters 

were disinfected prior to insertion using a 0.5-percent solution of chlorohexidine diacetate (Nolvasan, 

Fort Dodge Animal Health, Fort Dodge, Iowa) and then rinsed twice in sterile water. Sterile surgical 

gloves were worn during each surgery. 

To implant the tags, an incision approximately 7 mm long was made 5 mm anterior to the pelvic 

girdle and 3 mm away from and parallel to the mid-ventral line. The incision was made only deep 

enough to penetrate the peritoneum, using extra care so as not to damage vital organs. After the PIT tag 

was inserted into this incision, a shielded needle (Nipro I.V., 20-gauge × 5 cm) was used to guide the 

radio transmitter’s antenna through the body wall of the fish, as described by Ross and Kleiner (1982). 

Once the radio transmitter was in position, one to three simple, interrupted absorbable sutures (Ethicon 

coated vicryl braided suture 5-0, reverse cutting P-3 needle) were used to close the incision. 

Following surgery, each fish was placed in a recovery bath of fresh river water until it regained 

equilibrium. Fish were then transferred to net pens (1.2 × 0.61 × 0.61 m with 5 mm bar mesh) moored in 

the Klamath River near the Iron Gate Hatchery adult ladder entrance and held overnight to monitor 

recovery and ensure proper functioning of the radio transmitter. Fish were released after nautical 

twilight the following day to limit predation risk. 

Data Analysis

Detections from the PIT and radio systems were used to estimate detection probability of the PIT 

tag detection system. Data from the radio system was reviewed to remove false positive records using 

methods described in Beeman and others (2008). Their methods result in retaining records that are from 

a transmitter released as part of the study, at a time after fish release, and with at least two detections 

within a 10-min period. Lastly, if a fish was detected on both the PIT and radio systems, detection of the 

fish at the PIT tag detection system must occur prior to the detection at the radio system. Detections 

from the PIT tag detection system any time after release were assumed to be true positive records. The 

study period used for analysis was inclusively from June 2 to August 10, 2011. This period spans the 

time from the date following the first release date to the last date of PIT tag detection system operation

and includes 70 d from the last release date. 

The detection probability of the primary PIT tag detection system was estimated using CormackJolly-Seber mark-recapture methods (Cormack, 1964; Jolly, 1965; Seber, 1965). Detection of a tagged 

fish is a function of the joint probability of survival and detection, so these parameters must be 

estimated separately. This was done using the “recaptures only” data type in Program Mark (White and 

Burnham, 1999). The analysis was based on four occasions and three periods. The occasions include 

release, the primary PIT detection system, and the two radio-detection systems. The intervals include 

release to the primary PIT tag detection system, the primary PIT tag detection system to the first radio 

system, and the first radio system to the second radio system. The radio systems were identical to one 

another and monitored the same spatial and temporal areas, so the survival between the two radio 

systems (the third interval) was assumed to be 1.0 and was fixed to that value for analysis. The estimate 

of detection probability of the primary PIT tag detection system was based on a model allowing 

detection probabilities to vary independently among occasions and survival probabilities to vary 

independently among intervals. 
9 

Detection Probabilities

One study fish was detected by the primary PIT tag detection system and 23 were detected at the 

radio-telemetry systems. No fish were detected by the secondary PIT tag detection system installed on 

the frame net. The three fish released with only PIT tags were not detected. The study fish that was 

detected by the PIT tag detection system was detected once at PIT antenna 2 at 9:28:05 p.m. on June 8, 

2011, and was detected a total of 18 times on the two radio systems between 1:21:46 a.m. and 1:27:45 

a.m. on June 9, 2011. The 23 study fish detected by the radio systems were detected between June 7 and 

June 14, 2011. An additional eight fish from other studies were detected by the PIT tag detection system

1–28 times each (appendix 1). Six of the tags detected were from the 267 juvenile coho salmon tagged 

and released in the Shasta River by the California Department of Fish and Game (Chris Adams, written 

commun., November 16, 2011). Three of the nine fish detected by the PIT tag detection system were 

detected more than once. Of the 44 total detections, 22.7 percent were at antenna 1, 68.2 percent were at 

antenna 2, and 9.1 percent were at antenna 3. No fish were detected at antennas 4, 5, or 6. The disparity 

in detections between antennas 1–3 and 4–6 may indicate that more fish were passing near the river left 

shore, detection probabilities were different among antennas, or a combination of both. 

The detection probability of the PIT tag detection system was low. The capture histories of the 

fish implanted with both PIT and radio tags are listed in appendix 2. The estimate of the PIT tag 

detection system detection probability was 0.043 (SE = 0.042), with a 95-percent profile-likelihood 

confidence interval of 0.002–0.178. The estimate of survival from release to the PIT tag detection 

system was 0.535 (SE = 0.076), with a 95-percent profile-likelihood confidence interval of 0.387–0.679. 

There was no mortality in the sample between the PIT tag detection system and the radio system, so the 

survival from release to the radio system was the same as the survival from release to the PIT tag 

detection system. All fish detected by one radio system also were detected by the other system, 

indicating detection probability of the first radio array was 1.0. 

Discussion

The detection probability of the PIT tag detection system was much lower than expected. The 

system was installed in late summer 2010 when the water depth was low and the system was required to 

remain intact until testing with tagged fish in June 2011, when the water depth was much too deep for 

the in-water work required for PIT antenna installation. The system was compromised by the failure of 

two of the antenna power cables prior to the study period and high water levels during the study period. 

The antenna failures occurred between March 25, 2011, and April 7, 2011, which coincided with peak 

discharges. The failed antennas (antennas 5 and 6) were between the river thalweg and the shoreline. 

The discharge at USGS gaging station 11516530 near Iron Gate Dam was an average of 1,672.0 ft3

/s 

(range 1,020–3,410 ft3

/s) during the study period. The low detection probability is not typical of other 

systems. Connolly and others (2008) estimated the system they used detected 96–100 percent of the 

passing tagged fish. Their system was used in a stream and consisted of three lines of six antennas (3 × 

6) across a mean depth of 5–39 cm. We estimate the depth over the PIT tag detection system in this 

study was 1.5–1.8 m on June 1, 2011. That was likely the greatest depth during the study period because 

the river discharge decreased with time (fig. 2). We determined empirically that the read range of our 

PIT tag detection system was 35–41 cm, which is similar to the 45 cm range reported by Connolly and 

others (2008). 
10

The estimates of survival probability of the PIT- and radio-tagged fish was slightly lower than 

estimates from earlier studies in the Klamath River. For example, the range in estimated survival of 

radio-tagged yearlong coho salmon of hatchery origin from release near Iron Gate Hatchery to the Scott 

River was 0.576–0.894 during studies in 2007–09 (Beeman, 2008; Beeman and Juhnke, 2009; Beeman 

and others, 2009) compared to 0.535 (SE = 0.076) from this study. 

Detection probabilities of PIT antenna systems are affected by several factors. These include 

ambient electromagnetic fields, changes in water temperature and conductivity, presence of more than 

one tag in the antenna field at a time, and distance between the tag and the antenna (Zydlewski and 

others, 2006). Of these, the PIT tag detection system we evaluated likely was affected only by the 

distance between the tag and the antenna. The read ranges of test tags used at the pass-by antennas were 

35–41 cm and the read ranges of the pass-through antennas were slightly larger. These read ranges are 

consistent with the performance of other systems (Connolly and others, 2008). It is also unlikely that tag 

detections were hindered by multiple tags being present at an antenna at the same time, given the small 

number of tagged fish from this and other studies in the area. Effects of changes in water temperature or 

conductivity also are unlikely in this case because the receiver we used was a self-tuning type. Water 

depth over the antennas is known to negatively affect detection probability of juvenile salmonids (that 

is, non-benthic fish) due to the relatively small read range of PIT tag detection systems (Connolly and 

others, 2008). Water depth over the antennas likely would be less of a problem for fish traveling close to 

the river bottom, such as adult salmonids. We estimate that the water depth over the antennas was 1.5–

1.8 m, which is several times the read ranges we measured. Connolly and others (2008) noted a 

difference in PIT tag detection system detection probability between data collected at water depths less 

than 16 cm and at water depths greater than 16 cm. 

Detection probabilities of PIT tag detection systems also vary with the design. Pass-by antennas 

have shorter read ranges than pass-through antennas because pass-by antennas are laid flat on the 

substrate and fish can pass by only on one side. However, pass-by antennas pose less of an obstruction 

to water and debris passage than pass-through antennas, and are more resistant to damage from these 

sources (Zydlewski and others, 2006). We chose to design the system as a series of pass-by antennas for 

this reason. The addition of the pass-through antennas near one shoreline was opportunistic due to the 

damage two of the original antennas and the high water present prior to release of the fish. 

The results of this study suggest a series of PIT antennas placed in a shallower area, or a similar 

system used during a lower river stage height, would be required to achieve higher detection 

probabilities for studies of juvenile salmonids in the Klamath River. Antennas placed across all or part 

of the river in a series like the system described by Connolly and others (2008) could increase detection 

probability over a single line of detectors. The expected detection probability of a system of multiple 

detection arrays spanning the river can be estimated with the equation 

,)ˆ 1(1 N Psystem −−= Parray (1)

where N is the number of individual detection arrays spanning the river. If the single-system detection 

probability from this study were assumed (0.043), the expected total system detection probabilities for 

PIT-tagged juvenile coho salmon under conditions during this study would be 0.084 for two systems, 

0.124 for three systems, and 0.161 for four systems. The two largest uncertainties in deploying such a 

system in the Klamath River would be system damage from high discharge or debris loads, and the 

water depth over the antennas. Antennas of a lower-profile design, such as the flat-plate design 

described by Nunnallee and others (1998), or partially submerging the antennas into the substrate may 

reduce damage. Deployment sites expected to minimize water depth over the antennas during the 

desired study period also would be required to improve detections of juvenile salmonids. 
11

The use of an active telemetry system to evaluate the PIT detection system was efficient. We 

used the radio-telemetry system to estimate detection probability of the PIT detection system because 

the radio-telemetry system had been shown to have high detection probability in the study area (Beeman 

and others, 2008). In this study, the detection probability of the upstream radio array was 1.0. Use of a 

system with a high detection probability increases the information used from each fish and decreases the 

number of fish needed. We could have used a secondary PIT detection system to estimate the detection 

probability of the primary PIT detection system evaluated in this study, but if the detection probability 

of the secondary system was similar to that of the primary system, we likely would have detected only 

23*0.043 = 1 PIT-tagged fish on the secondary array rather than the 23 detected at the radio-telemetry

detection system, resulting in little information with which to evaluate the primary system. An estimated

total of 23/0.043 = 538 PIT-tagged fish would have been required to achieve the same precision in 

detection probability as we achieved by releasing 43 PIT-tagged and radio-tagged fish if a secondary 

PIT detection system were used rather than the radio–telemetry detection system.

In summary, the PIT detection system evaluated in 2011 was damaged during high river 

discharges and the detection probability was lower than expected. Damage from high water velocities 

could be mitigated in future deployments by using antennas with a low-profile design, or by burying the 

antennas into the substrate. The detection probabilities of juvenile coho salmon likely were affected 

negatively by the high river stage during the study period. Detection probabilities of all fishes could be 

increased by using a series of antenna systems spanning the river and those of pelagic fish can be 

expected to increase under conditions of shallow water over the antennas. PIT antennas near the river 

bottom may work well for other species or life stages present close to the river bottom, such as adult 

salmonids. 

Acknowledgments

We thank the California Department of Fish and Game staff at the Iron Gate Fish Hatchery for 

providing fish and space for this study. Chris Adams of the California Department of Fish and Game 

assisted with PIT tag detection system maintenance, and Philip Haner of the U.S. Geological Survey 

designed and oversaw the installation of the radio-telemetry detection system. We also thank Darcy 

Derry for allowing the primary PIT tag detection system to be installed on private land. The document 

was improved by review comments from Bill Muir and Pat Connolly. The Bureau of Reclamation 

funded the study under interagency acquisition number R10PG20183. 

References Cited

Adams, N.S., Rondorf, D.W., Evans, S.D., and Kelley, J.E., 1998, Effects of surgically and gastrically 

implanted radio transmitters on growth and feeding behavior of juvenile Chinook salmon: 

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13

Appendix 1. Detections of PIT Tags from Other Studies. 

[These data are from the PIT tag detection system installed at Klamath River kilometer 252.7 and operated from June 1 to 

August 10, 2011]

Detection time Antenna Detection Antenna

Tag identifier (mm/dd/yyyy hh:mm:ss) No. Tag identifier time No.

3D6.00084E2AA1 08/06/2011 01:56:20 PM 3 3D9.1C2D2836A8 06/05/2011 06:59:03 PM 2

3D9.1C2D18D911 07/11/2011 05:16:43 PM 1 3D9.1C2D2836A8 06/05/2011 07:04:09 PM 2

3D9.1C2D18D911 07/11/2011 05:16:45 PM 2 3D9.1C2D2836A8 06/05/2011 07:09:11 PM 2

3D9.1C2D18D911 07/11/2011 05:25:05 PM 2 3D9.1C2D2836A8 06/05/2011 07:14:13 PM 2

3D9.1C2D18D911 07/11/2011 05:25:07 PM 1 3D9.1C2D2836A8 06/05/2011 07:14:56 PM 1

3D9.1C2D18D911 07/11/2011 05:37:23 PM 2 3D9.1C2D2836A8 06/05/2011 07:19:45 PM 2

3D9.1C2D18D911 07/11/2011 05:40:18 PM 1 3D9.1C2D2836A8 06/05/2011 07:25:07 PM 2

3D9.1C2D18D911 07/11/2011 05:46:18 PM 2 3D9.1C2D2836A8 06/05/2011 07:30:08 PM 2

3D9.1C2D18D911 07/11/2011 05:48:26 PM 1 3D9.1C2D2836A8 06/05/2011 07:36:21 PM 2

3D9.1C2D18DD6D 06/25/2011 09:45:46 AM 1 3D9.1C2D2836A8 06/05/2011 07:41:45 PM 2

3D9.1C2D18DD6D 06/25/2011 09:54:46 AM 2 3D9.1C2D2836A8 06/05/2011 07:46:59 PM 2

3D9.1C2D18E559 06/29/2011 02:27:30 AM 2 3D9.1C2D2836A8 06/05/2011 07:52:00 PM 2

3D9.1C2D1FE53A 07/21/2011 05:22:08 AM 3 3D9.1C2D2836A8 06/05/2011 07:59:23 PM 2

3D9.1C2D282416 06/23/2011 03:38:31 AM 3 3D9.1C2D2836A8 06/05/2011 08:05:18 PM 2

3D9.1C2D2836A8 06/05/2011 06:17:31 PM 2 3D9.1C2D2836A8 06/05/2011 08:16:29 PM 2

3D9.1C2D2836A8 06/05/2011 06:25:25 PM 2 3D9.1C2D2836A8 06/05/2011 08:21:33 PM 2

3D9.1C2D2836A8 06/05/2011 06:30:43 PM 2 3D9.1C2D2836A8 06/05/2011 08:29:58 PM 1

3D9.1C2D2836A8 06/05/2011 06:32:00 PM 1 3D9.1C2D2836A8 06/05/2011 08:30:32 PM 2

3D9.1C2D2836A8 06/05/2011 06:38:13 PM 2 3D9.1C2D2836A8 06/05/2011 08:42:42 PM 1

3D9.1C2D2836A8 06/05/2011 06:43:33 PM 2 3D9.1C2D2836A8 06/05/2011 08:50:38 PM 1

3D9.1C2D2836A8 06/05/2011 06:48:33 PM 2 3D9.1C2D2869C7 06/14/2011 11:40:00 PM 3

3D9.1C2D2836A8 06/05/2011 06:53:44 PM 2
14

Appendix 2. Capture Histories of PIT- and Radio-Tagged Yearling Coho Salmon 

from Iron Gate Hatchery Used to Evaluate a PIT Detection System in the Klamath 

River, 2011. 

[The four occasions are release, the primary PIT detection system, and each of two identical radio detection systems. A '1' in 

a column indicates detection (or release) and '0' indicates no detection]

Encounter Observed

history count

1111 1

1011 22

1000 20
Publishing support provided by the U.S. Geological Survey

Publishing Network, Tacoma Publishing Service Center

For more information concerning the research in this report, contact the 

Director, Western Fisheries Research Center

U.S. Geological Survey

6505 NE 65th Street

Seattle, Washington 98115

http://wfrc.usgs.gov/
Beeman and others—Detection Probability of an In-Stream PIT Tag Detection System for Juvenile Salmonids, Klamath River, California, 2011—Open-File Report 2012-1001