Prepared in cooperation with the Bureau of Reclamation

Monitoring of Adult Lost River and Shortnose Suckers in 

Clear Lake Reservoir, California, 2008–2010

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2013–1301

Monitoring of Adult Lost River and Shortnose Suckers in 

Clear Lake Reservoir, California, 2008–2010

By David A. Hewitt and Brian S. Hayes

Prepared in cooperation with the Bureau of Reclamation 

Open-File Report 2013-1301

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:

Hewitt, D.A., and Hayes, B.S., 2013, Monitoring of adult Lost River and shortnose suckers in Clear Lake 

Reservoir, California, 2008–2010: U.S. Geological Survey Open-File Report 2013-1301, 18 p., 

http://dx.doi.org/10.3133/ofr20131301.

ISSN 2331-1258 (online)

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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

Executive Summary....................................................................................................................................... 1

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

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

Study Site................................................................................................................................................... 3

Fall Sampling, 2008 and 2009 ................................................................................................................... 3

Spring Sampling, 2009 and 2010............................................................................................................... 4

Results........................................................................................................................................................... 4

Catch Summary ......................................................................................................................................... 4

Detections Summary.................................................................................................................................. 4

Lost River Suckers..................................................................................................................................... 5

Shortnose Suckers..................................................................................................................................... 6

Discussion ..................................................................................................................................................... 7

Acknowledgments ......................................................................................................................................... 9

References Cited........................................................................................................................................... 9

Figures

Figure 1. Map showing location of Clear Lake Reservoir (Clear Lake) in the Upper Klamath River Basin of 

southern Oregon and northern California .................................................................................................... 12

Figure 2. Detections of Lost River suckers on the remote passive integrated transponder (PIT) tag 

antennas in Willow Creek during the spring spawning seasons in 2006–2010............................................ 13

Figure 3. Length frequencies of male and female Lost River suckers captured with trammel nets in Clear 

Lake Reservoir during fall sampling, 2004–2009......................................................................................... 14

Figure 4. Detections of shortnose suckers on the remote passive integrated transponder (PIT) tag 

antennas in Willow Creek during the spring spawning seasons in 2006–2010............................................ 15

Figure 5. Length frequencies of male and female shortnose suckers captured with trammel nets in Clear 

Lake Reservoir during fall sampling, 2004–2009......................................................................................... 16

Tables

Table 1. Catches of Lost River and shortnose suckers in fall trammel net sampling in Clear Lake Reservoir, 

California, 2006–2009.................................................................................................................................. 17

Table 2. Number of Lost River and shortnose suckers PIT-tagged in fall trammel net sampling and the 

number of individuals detected on remote antennas in Willow Creek during spring spawning migrations, 

2006–2010................................................................................................................................................... 18
iv

Conversion Factors

SI to Inch/Pound

Multiply By To obtain

Length

millimeter (mm) 25.4 inch (in.)

centimeter (cm) 2.54 inch (in.)

meter (m) 3.281 foot (ft) 

meter (m) 1.094 yard (yd) 

kilometer (km) 0.6214 mile (mi)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32.
1

Monitoring of Adult Lost River and Shortnose Suckers 

in Clear Lake Reservoir, California, 2008–2010

By David A. Hewitt and Brian S. Hayes

Executive Summary

In collaboration with the Bureau of Reclamation, the U.S. Geological Survey began a 

consistent monitoring program for endangered Lost River suckers (Deltistes luxatus) and 

shortnose suckers (Chasmistes brevirostris) in Clear Lake Reservoir, California, in the fall of

2004. The program was intended to develop a more complete understanding of the Clear Lake 

Reservoir populations because they are important to the recovery efforts for these species. We 

report results from this ongoing program and include sampling efforts from fall 2008 to spring 

2010. We summarize catches and passive integrated transponder (PIT) tagging efforts from 

trammel net sampling in fall 2008 and fall 2009, as well as detections of PIT-tagged suckers on 

remote antennas in the spawning tributary, Willow Creek, in spring 2009 and spring 2010.

Trammel net sampling resulted in a relatively low catch of suckers in fall 2008 and a high 

catch of suckers in fall 2009. We attribute the high catch of suckers to low lake levels in 2009, 

which concentrated fish. As in previous years, shortnose suckers made up the vast majority of 

the sucker catch and recaptures of previously PIT-tagged suckers were relatively uncommon. 

Across the 2 years, we captured and tagged 389 new Lost River suckers and 2,874 new shortnose 

suckers. Since the program began, we have tagged a total of about 1,200 Lost River suckers and 

5,900 shortnose suckers that can be detected on the remote antennas in Willow Creek. Detections 

of tagged suckers were low in both spring 2009 and spring 2010. The magnitude of the spawning 

migration was presumably small in both years because of low flows in Willow Creek; detections 

were similar to a previous low-flow year (spring 2007) and much lower than previous years with 

higher flows (spring 2006 and spring 2008).

The size composition of fish captured in fall trammel net sampling over time suggests 

that the Lost River sucker population probably has decreased in abundance from what it was in 

the early 2000s. Shortnose suckers are smaller than Lost River suckers, and we are unable to 

infer any trend in abundance for shortnose suckers because it is impossible to separate

recruitment of small fish from size selectivity of the trammel nets. Nonetheless, the substantial 

catch of small shortnose suckers in 2009, especially females, indicates that some new individuals 

recruited to the population.

Problems with inferring status and population dynamics from size composition data can 

be overcome by a robust capture-recapture program that follows the histories of PIT-tagged 

individuals. Inferences from such a program are currently hindered by poor detection rates 

during spawning seasons with low flows in Willow Creek, which indicate that a key assumption 

of capture-recapture models is violated. We suggest that the most straightforward solution to this 

issue would be to collect detection data during the spawning season using remote PIT tag 

antennas in the strait between the west and east lobes of the lake.
2

Introduction

Lost River suckers (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) are 

federally endangered catostomids endemic to the Upper Klamath Basin of southern Oregon and 

northern California. Both species are long-lived; Terwilliger and others (2010) reported a Lost 

River sucker aged at more than 50 years old and Scoppettone and Vinyard (1991) reported 

shortnose suckers as old as 33 years. Historical accounts indicate that both species once were 

extremely abundant throughout the Upper Klamath Basin and were harvested in both a Native 

American subsistence fishery and a recreational snag fishery (Cope, 1884; Gilbert, 1898; 

Golden, 1969; Rasmussen, 2011). Evidence for decreasing population sizes and range reductions 

were noted as early as the mid-1960s, but the extent of the problem was not evident until the 

mid-1980s when recreational catch rates decreased substantially (Bienz and Ziller, 1987; 

Cooperman and Markle, 2003; National Research Council, 2004). The recreational snag fishery 

was closed in 1987, and in 1988 both species were listed as endangered by the U.S. Fish and 

Wildlife Service under the Endangered Species Act (USFWS, 1988).

Although the populations of Lost River and shortnose suckers in Upper Klamath Lake, 

Oregon, have received the most research attention, Clear Lake Reservoir in Modoc County, 

California (hereafter, Clear Lake) supports self-sustaining populations of each species that have

been identified as critical to recovery efforts (USFWS, 2012). The life history, spawning 

biology, and status of Lost River and shortnose sucker populations in Upper Klamath Lake are 

reasonably well studied (Buettner and Scoppettone, 1990; Scoppettone and Vinyard, 1991; 

Perkins and others, 2000b; Cooperman and Markle, 2003; Janney and others, 2008; Hewitt and 

others, 2012). In contrast, the populations in Clear Lake are less well studied. Data collected by 

Andreasen (1975) and Koch and others (1975) more than 35 years ago indicated that the 

populations were in decline. In contrast, research in the last 20 years indicated that both species 

were abundant in Clear Lake and that the populations were characterized by diverse age 

structures (Buettner and Scoppettone, 1991; Scoppettone and others, 1995; USFWS, 2002).

In collaboration with the Bureau of Reclamation, the U.S. Geological Survey began a 

long-term study at Clear Lake in fall 2004 to monitor sucker spawning migrations and to assess 

the feasibility of estimating survival and related parameters with capture-recapture methods. The 

study consists of two types of sampling: (1) trammel net sampling in the fall to capture and tag 

adult suckers with passive integrated transponder (PIT) tags; and (2) sampling in the spring with

remote underwater PIT tag antennas placed in Willow Creek to monitor the spawning migrations 

of tagged fish. In this report, we describe ongoing research efforts for endangered suckers in 

Clear Lake and summarize data from sampling that occurred from fall 2008 to spring 2010 in 

order to address four objectives: (1) describe the species composition of fall trammel net catches; 

(2) determine sex ratios for each population; (3) describe the timing of the spawning migrations 

for each species based on detections of PIT-tagged fish in Willow Creek; and (4) characterize the 

status of the populations to the extent possible based on the size composition of suckers captured 

in fall trammel net sampling.
3

Methods

Study Site

Clear Lake is part of the Lost River subbasin that spans the Oregon-California border 

(fig. 1). Clear Lake is a natural lake that was enlarged by the Bureau of Reclamation with a dam 

completed in 1910. The dam was built to control water flows in the Lost River and reduce flows

into the reclaimed portions of Tule Lake. The reservoir also provides irrigation water for 

agricultural operations in the Lost River subbasin. Clear Lake has distinct east and west lobes 

that are connected in the north through a shallow strait with a narrow channel. Water is deeper in 

the west lobe (up to 4 m) than in the east lobe (less than 2 m), and the east lobe typically is low 

enough in the late summer and fall to make boat travel difficult. The spawning tributary for Lost 

River and shortnose suckers is Willow Creek, which enters the reservoir in the northeastern

corner of the east lobe near Clear Lake Dam.

Fall Sampling, 2008 and 2009

Adult suckers were sampled in the west lobe of Clear Lake on 12 days between 

September 15 and October 2, 2008, and on 14 days between September 23 and October 15, 2009.

Beginning between 0730 and 0900 hours on each day, each of two boat crews deployed four to 

six large trammel nets (net dimensions: 91.4 m long × 1.8 m deep; two 30.5-cm bar mesh outer 

panels and one 3.8-cm bar mesh inner panel). Locations for net sets were chosen to focus 

sampling effort along the shoreline in the southern one-half to two-thirds of the west lobe, where 

sucker catches are consistently highest. Nets were occasionally set in the northern part of the 

west lobe as well. Nets were set perpendicular to shore beginning as close to shore as possible;

distance from shore for a given set was influenced to some extent by prevailing winds. The first 

set of nets was allowed to soak for about 2 hours before being retrieved, at which time captured 

suckers were removed from the nets and transferred to floating net pens. After all suckers were 

transferred to net pens, the nets were set a second time at new locations and the crews returned to 

process fish captured in the first sets. Overall, a sampling day resulted in 16–24 net sets, and we 

set a total of 264 and 297 nets in 2008 and 2009, respectively.

During processing, the species and sex of each sucker was determined based on external 

characteristics (Markle and others, 2005) and each fish was measured to the nearest millimeter 

fork length (FL). Suckers were scanned for the presence of a PIT tag and untagged fish were 

injected with a tag in the ventral abdominal musculature anterior to the pelvic girdle. We used 

tags operating at 125 kilohertz (kHz) prior to fall 2005, but all fish collected in 2005 through 

2009 were tagged with 134 kHz full-duplex tags because of the improved read range of the 

higher frequency tags. Recaptured fish that had been previously tagged with 125 kHz tags were 

re-tagged with 134 kHz tags because the remote antennas in Willow Creek were only able to 

detect the higher frequency tags.

We compared length composition data from our fall 2008 and fall 2009 sampling with 

length composition data collected in previous years. A previous report included length 

composition data as far back as 1993 (Barry and others, 2009). In this report, we include data 

since 2004, following the demographic transition that apparently occurred in the late 1990s and 

early 2000s.
4

Spring Sampling, 2009 and 2010

The operation of remote PIT tag antennas in Willow Creek was incorporated into the 

study beginning in spring 2006, and these efforts were continued through spring 2010. As in 

previous years, antennas were installed in Willow Creek about 3 km upstream of where it enters 

Clear Lake. Six large rectangular antennas were placed in an upright, pass-through orientation 

and located end to end to cover the entire width of the channel (antenna dimensions: 3 m long × 

0.75 m tall). Antennas were connected to a transceiver (Digital Angel model FS1001M) located 

on shore with water-tight cables. The transceiver recorded the date, time, and identification code 

of PIT-tagged suckers that swam through the antennas.

Antennas were installed on January 22, 2009, and on January 28, 2010, early enough to 

monitor the complete spawning migrations. Suckers that had been previously tagged with 134 

kHz PIT tags were detected by the antennas as they ascended the creek, providing information 

about the timing of spawning runs. Because the timing of spawning runs appears to be controlled 

in part by water temperature, we installed temperature loggers in the middle of the water column 

at the antenna site to record water temperature at hourly intervals. We were not able to recover 

the temperature loggers in 2010, so we do not have data for that spawning season. In 2009, the 

last detection of a sucker was recorded on May 9, and the antennas were removed on May 29. In 

2010, the last detection was recorded on June 13 and the antennas were removed on June 30.

Results

Catch Summary

We captured a total of 926 endangered suckers in fall 2008 and 2,531 in fall 2009 (table 

1). The vast majority of suckers captured in 2008 and 2009 were shortnose suckers (73 percent in 

2008; 86 percent in 2009). Lost River suckers made up about 11 percent of the catch in both 

years and the remainder of the catch was composed of Klamath largescale suckers (Catostomus 

snyderi) and suckers that could not be identified to species. We captured more suckers in 2009 

than in any previous year, which we attribute in part to the low water levels in the west lobe that 

fall. Water surface elevation was nearly 0.6 m lower during sampling in fall 2009 than during 

sampling in any other year since 2006, and our impression is that the low water level 

concentrated fish. 

For all species in all years since 2006, only a small percentage of captured suckers had 

been previously tagged (table 1). Shortnose suckers have consistently had the highest percentage 

of recaptures, and recaptures made up 6 percent of the shortnose sucker catch in both 2008 and 

2009. No more than 1 percent of Lost River suckers had been recaptures prior to 2009, but 3.6 

percent were recaptures in that year.

Detections Summary

The remote antennas in Willow Creek detected 146 PIT-tagged Lost River and shortnose 

suckers in spring 2009 and 286 PIT-tagged individuals in spring 2010 (table 2). The total number 

of individuals detected on the remote antennas in both years was similar to 2007 and was much 

lower than in 2006 or 2008, despite more fish being tagged (Barry and others, 2009). Although 

Willow Creek does not have a flow gage, snowpack in the watershed was minimal in both 2009 

and 2010 and we observed that flows were low during both spawning seasons. The low flows in 

the spawning tributary explain the overall low number of fish detected by the remote antennas, a 
5

pattern we have observed since 2006. An isolated precipitation event occurred in late April 2010, 

which apparently increased flows for a short time and led to a late pulse of migrating fish, 

particularly shortnose suckers (figs. 2 and 4).

Suckers PIT-tagged in 2005 continued to be detected in numbers comparable to fish 

tagged in later years (table 2). For example, the number of shortnose suckers from the 2005 

tagging cohort that were detected in spring 2009 was nearly the same as the number of shortnose 

suckers detected from the 2007 and 2008 tagging cohorts. The only exception was shortnose 

sucker detections in 2010, which were dominated by fish newly tagged in the large catches 

during fall 2009 trammel net sampling. Lost River sucker detections are consistently low, but 

represent generally similar proportions of the tagging cohorts when compared to shortnose 

suckers. Although the detections in Willow Creek are strongly influenced by flows, the pattern of 

detections indicates that many PIT-tagged fish remain at large and a future year with high flows

like 2008 could generate a substantial number of detections.

Lost River Suckers

Since our contemporary monitoring program began in fall 2004, we have PIT-tagged 

approximately 1,360 Lost River suckers. Although we have recaptured and re-tagged some of the 

fish tagged with 125 kHz PIT tags in 2004, about 160 fish from that cohort potentially remain at 

large with 125 kHz tags and can not be detected on the remote antennas in Willow Creek. In 

addition to the fish we have tagged since 2004, a substantial number of juveniles and adults were 

tagged with 125 kHz PIT tags in 1993–1996 and 2000. We suspect that few of those fish remain 

at large in the population, and we did not recapture any of them in our fall trammel net sampling 

between 2004 and 2009.

The sex ratio of Lost River suckers captured in fall trammel net sampling was skewed to 

females in 2008 and nearly even in 2009 (table 1). With the exception of 2006 and 2009, the sex 

ratio in trammel net sampling has been skewed to females (see also Barry and others, 2006). 

Although most of the PIT-tagged Lost River suckers are females, the detections on the remote 

antennas in Willow Creek tend to favor males (table 2).

The number of remote detections of Lost River suckers in Willow Creek was low in both 

2009 and 2010. The seasonal pattern of detections in 2009 was similar to the pattern in earlier 

years, with most detections occurring in March (fig. 2). The water temperature records show that, 

similar to past years, detections in 2009 increased when water temperatures increased to greater 

than 6°C. In 2010, nearly all of the 28 Lost River suckers that were detected in Willow Creek 

migrated past the antennas with the short-term increase in flows that occurred in late April and 

early May.

In a previous report, we presented length composition data from trammel net catches 

dating back to 1993 (Barry and others, 2009). That data showed that the spawning population of 

Lost River suckers “turned over,” transitioning from a relatively homogeneous population of 

larger, presumably older individuals to one comprised of smaller, presumably younger 

individuals. The transition occurred over a relatively short time frame between 1996 and the 

early 2000s, suggesting that the older individuals spawned the newer individuals not long before 

they died off. A similar transition occurred in the mid-1990s for the endangered sucker 

populations in Upper Klamath Lake (Janney and others, 2008). Whereas the changes in Upper 

Klamath Lake were due at least in part to extensive fish die-offs in 1995, 1996, and 1997 

(Perkins and others, 2000a), no conclusions have been drawn about the cause(s) for the transition

in Clear Lake. The updated series of length frequencies for Lost River suckers from Clear Lake
6

indicates that the new cohort of small individuals that were first captured in 2000 have remained 

the dominant cohort of spawners through 2009 (fig. 3). By 2009, the median FL of males was 

504 mm and the median FL of females was 528 mm, still substantially smaller than the fish that 

were present in the mid-1990s (Barry and others, 2009). A large cohort of new individuals were 

apparent in our sampling in 2007, but the vast majority of these individuals apparently died in 

the last couple of years and are no longer a substantial part of the population. Lost River suckers 

do not grow fast enough in Clear Lake (Barry and others, 2009) to allow the smaller fish from

2007 to have grown into the dominant cohort of larger fish in 2008 and 2009.

Shortnose Suckers

We have PIT-tagged approximately 6,240 shortnose suckers since fall 2004. Although we 

have recaptured and re-tagged some of the fish tagged with 125 kHz PIT tags in 2004, about 330 

fish from that cohort potentially remain at large with 125 kHz. In addition to the fish we have 

tagged since 2004, a substantial number of juveniles and adults were tagged with 125 kHz PIT 

tags in 1992–1996 and 2000. We suspect that few of those fish remain at large in the population, 

but we did recapture (and re-tag) 16 of them in our fall trammel net sampling between 2004 and 

2009. Eight of those individuals were at large for 10 or more years before being recaptured. Four 

individuals were measured at between 100 and 150 mm in length when they were first PITtagged in 1995 and 1996, and had grown to be 310 to 430 mm FL by the time they were 

recaptured.

As in previous years, the sex ratio of shortnose suckers captured in fall trammel net 

sampling was strongly skewed to females in 2008 and 2009. Catches of female shortnose suckers 

have consistently been as much as two or three times the catches of males since 2004 (see also 

Barry and others, 2006). In contrast to results for Lost River suckers, sex ratios for the detections 

of shortnose suckers on the remote antennas in Willow Creek have reflected the sex ratio of the 

tagged population (table 2).

The number of remote detections of shortnose suckers in Willow Creek was low in 2009, 

but detections occurred through March and April as in past years (fig. 4). In 2010, few detections 

occurred during the low flows in March and April, but a surge in detections occurred in late 

April and early May, coinciding with the increased flows from an isolated precipitation event. 

More than one-half of the shortnose suckers detected in 2010 migrated past the antennas in the 

first 3 days of May. Similar to Lost River suckers and the data from previous years, detections in 

2009 first occurred when water temperatures reached about 6°C.

Similar to Lost River suckers, the long-term series of length composition data showed 

that the shortnose sucker population in Clear Lake transitioned from a rather homogeneous

population of large, old individuals to one comprised of small, young individuals between 1996 

and the early 2000s (Barry and others, 2009). The updated series of length frequencies for

shortnose suckers captured in fall trammel net sampling shows that the cohort of small fish 

present in 2004 has remained the dominant cohort through 2009 (fig. 5). By 2009, the median FL

of males was 350 mm and the median FL of females was 375 mm, still somewhat smaller than 

the fish that were present in the mid-1990s (Barry and others, 2009). However, interpretation of 

length data for shortnose suckers is complicated by the selectivity of our trammel nets. 

Experience has shown that the effectiveness of our nets decreases for smaller fish approaching 

300 mm FL. Because of their smaller size, a larger proportion of the shortnose sucker population

coincides with the size range where trammel net effectiveness decreases, particularly if new 

individuals are recruiting to the population. As a cautionary example, we note the apparent 
7

“bulges” on the left side of the length frequencies from fall 2009 sampling; the bulge is 

particularly obvious for females (fig. 5). For shortnose suckers, it is impossible to determine 

based on length data alone the extent to which new individuals are contributing to fall trammel 

net catches.

Discussion

Fall trammel net sampling has been an effective strategy for capturing and PIT-tagging 

Lost River and shortnose suckers in Clear Lake. Through 2009, we have tagged more than 1,300 

Lost River suckers and more than 6,200 shortnose suckers. Although we are cautious about

drawing inferences from raw catch rates, the consistent difference in catches between the two 

species indicates that the population of shortnose suckers is substantially larger than the 

population of Lost River suckers. Despite the large number of tagged fish at large in the 

populations, physical recaptures of previously tagged individuals of either species have been 

relatively uncommon in fall trammel net sampling. In contrast, we have collected large numbers 

of detections of suckers tagged with 134 kHz tags on the remote antennas in Willow Creek in 

years with adequate flows during the spawning season (for example, 2008). Flows in Willow 

Creek were low in both 2009 and 2010 and detections on the remote antennas were low in both 

years.

Based on the size composition of fish captured in fall trammel net sampling over time, we 

conclude that the Lost River sucker population probably has decreased in abundance from what 

it was in the early 2000s. Since 2000, we have not observed any substantial number of new 

individuals surviving to contribute to the spawning population. The new cohort of small fish that 

was seen in 2007 apparently died off for unknown reasons before many of the individuals 

reached 400 mm FL. As a result, recruitment of new spawners probably has not balanced natural 

mortality. For shortnose suckers, we are unable to infer population trends based on size 

composition data alone because it is impossible to disentangle recruitment of small fish from size 

selectivity of the trammel nets. The catch of small shortnose suckers in 2009, especially females, 

suggests that new individuals were recruiting to the population, but the magnitude of that 

recruitment is unknown. We note that our conclusion in Barry and others (2009) that shortnose

suckers were experiencing an ongoing lack of recruitment, based on length data from trammel 

net sampling through fall 2007, was likely incorrect. Such issues of interpretation related to size 

composition data emphasize the benefits of a capture-recapture program that follows the histories 

of individual fish.

The main objective of our adult sucker research in Clear Lake has been to establish a 

capture-recapture program that can generate information on the status and dynamics of the 

sucker spawning populations, similar to that in Upper Klamath Lake (Janney and others, 2008; 

Hewitt and others, 2010, 2012). The primary impediment to inferences based on capturerecapture is that detection rates of PIT-tagged fish during spawning seasons with low flows in 

Willow Creek are much reduced compared to years when flows are higher. The poor detection 

rates are themselves a problem because they reduce the amount of data collected for capturerecapture, but they are even more troublesome because they indicate that a critical assumption of 

capture-recapture models is being violated—that each fish alive in the population has a chance of 

being reencountered in each sampling occasion. A key implication of this assumption violation is 

that any estimates of survival probabilities produced by the models will be negatively biased.

However, relatively minor changes to the sampling program could lead to substantial gains in 

our ability to make inferences about population dynamics through capture-recapture.
8

The most straightforward solution to the detections issue would be to collect detection 

data during the spawning season somewhere outside of Willow Creek. The obvious location for 

an array would be the strait between the west and east lobes of the lake. We expect that nearly all 

suckers return to the west lobe at some point during the summer or fall because of the low water 

levels in the east lobe at those times. Thus, fish migrating to spawn would have to pass through 

the strait to access spawning habitat in Willow Creek. Furthermore, even in years with high 

flows in Willow Creek, fish that do not migrate upstream as far as the antennas in Willow Creek 

would have an opportunity to be detected during the spawning season. A radio telemetry study 

would be one way to confirm the seasonal movements of suckers and understand the likely 

success of such an approach. Results from radio telemetry could determine whether some fish 

skip spawning in some years and how far upstream fish migrate during a season in which they do 

spawn.

Another possible change would be to shift trammel net sampling to coincide with the 

spawning season, such that all sampling for a year occurs in one time period as it does for sucker 

monitoring in Upper Klamath Lake (Hewitt and others, 2012). Such a change would only benefit 

capture-recapture inferences if it allowed us to recapture substantially more previously tagged

fish by targeting areas where they concentrate before, during, or after spawning. An additional 

benefit would be that sampling during the spawning season would make it easier to determine 

the sex of captured fish, particularly for shortnose suckers and Klamath largescale suckers, for 

which sex can be more difficult to ascertain. Nonetheless, sampling in Clear Lake in late winter 

and early spring can be especially challenging because of winter weather, road conditions, and 

the remoteness of the area. Indeed, these factors often create difficulties for installing the remote 

PIT tag antennas in Willow Creek early enough to be sure that we capture the entire time period 

of the sucker spawning migrations, which can begin in February. We suspect that shifting 

trammel net sampling to occur during the spawning season would not in itself provide sufficient 

data to support strong inferences from capture-recapture models.

Radio telemetry might also help explain the apparent discrepancy in sex ratios for Lost 

River suckers captured in fall trammel net sampling and those detected in Willow Creek during 

the spawning season. The sex ratio of Lost River suckers captured in fall trammel net sampling

since 2004, with the exception of 2006 and 2009, has favored females, similar to catches for the 

river-spawning subpopulation of this species in Upper Klamath Lake (Hewitt and others, 2012). 

As a result, more females than males have been tagged with 134 kHz PIT tags. However, the sex 

ratio of Lost River suckers detected on antennas in Willow Creek, with the exception of 2010 

when few fish were detected, has consistently favored males. This result contrasts with results 

for shortnose suckers, where catches and detections in both Upper Klamath Lake and Clear Lake 

are dominated by female fish. Possible explanations for the reduced detections of female Lost 

River suckers in Willow Creek include (1) lower detection probabilities compared to males; (2) 

lower survival compared to males; and (3) females skipping years between spawning events but 

males spawning every year.
9

Acknowledgments

We thank the numerous personnel from the USGS Klamath Falls Field Station for 

assistance with collecting and processing field data over many years. Alta Harris and Amari 

Dolan-Caret work diligently to maintain the integrity of the data set of PIT tag encounters. The 

report was improved by reviews from Summer Burdick and Nolan Banish. Funding was 

provided by the Bureau of Reclamation as part of its mission to manage, develop, and protect 

water and related resources in an environmentally and economically sound manner in the interest 

of the American public.

References Cited

Andreasen, J.K., 1975, Systematics and status of the family Catostomidae in southern Oregon: 

Corvallis, Oregon State University, Ph.D. thesis, 76 p.

Barry, P.B., Hayes, B.S., Janney, E.C., Shively, R.S., Scott, A.C., and Luton, C.D., 2006, 

Monitoring of Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) suckers in 

Gerber and Clear Lake Reservoirs, 2005–2006: Report for the Bureau of Reclamation, 

Klamath Basin Area Office, Oreg., U.S. Geological Survey, Klamath Falls Field Station, 

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dynamics of adult Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) 

suckers in Clear Lake Reservoir, California, 2006–08: U.S. Geological Survey Open-File 

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Klamath Lake, Oregon: Reno Field Station, Nev., National Fisheries Research Center, 108 p.

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status of the shortnose sucker (Chasmistes brevirostris) and Lost River sucker (Deltistes 

luxatus) in the Klamath River Basin, California: Report for the California Department of Fish 

and Game, Contract FG-8304, Reno Substation, Nev., Seattle National Fishery Research 

Center, 102 p.

Cooperman, M., and Markle, D.F., 2003, Rapid out-migration of Lost River and shortnose 

sucker larvae from in-river spawning beds to in-lake rearing grounds: Transactions of the 

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Basin, and of the Idaho Pliocene lake: Proceedings of the Academy of Natural Sciences of 

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Commission Central Region Administrative Report No. 1–69, 13 p.

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fisheries capture-recapture studies through remote detection of PIT tags: Fisheries, v. 35, p. 

217–231.
10

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of adult Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) suckers in 

Upper Klamath Lake, Oregon, 2011: U.S. Geological Survey Open-File Report 2012-1193, 

42 p.

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analysis of Lost River sucker and shortnose sucker populations in Upper Klamath Lake, 

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on the effects of proposed Klamath Project operations from May 31, 2013, through March 31, 

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life history of shortnose suckers (Chasmistes brevirostris) and Lost River suckers (Deltistes 

luxatus) in Tule and Clear Lakes: National Biological Service, Reno Field Station, Nev., and 

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11

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Bureau of Reclamation’s proposed 10-year operation plan for the Klamath Project and its 

effect on the endangered Lost River sucker (Deltistes luxatus), endangered shortnose sucker 

(Chasmistes brevirostris), threatened bald eagle (Haliaeetus leucocephalus), and proposed 

critical habitat for the Lost River and shortnose suckers: U.S. Fish and Wildlife Service, 

Klamath Falls Fish and Wildlife Office, Oreg., 204 p.

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Region, xviii + 122 p.
12

Figure 1. Map showing location of Clear Lake Reservoir (Clear Lake) in the Upper Klamath River Basin of 

southern Oregon and northern California. Willow Creek, the spawning tributary for Lost River and shortnose 

suckers, flows into Clear Lake from the east near the dam. Inset shows the area of the Klamath River 

watershed. Map modified and reprinted from National Marine Fisheries Service and U.S. Fish and Wildlife 

Service (2013), with permission.
13

Figure 2. Detections of Lost River suckers on the remote passive integrated transponder (PIT) tag 

antennas in Willow Creek during the spring spawning seasons in 2006–2010. If an individual fish was 

detected more than once in a given season, only the first detection is included. Average daily water 

temperature (°C) was taken from in-stream loggers at the antenna site in 2007, 2008, and 2009.
14

Figure 3. Length frequencies of male and female Lost River suckers captured with trammel nets in Clear 

Lake Reservoir during fall sampling, 2004–2009. Dots on the x-axis in each panel show the median fork 

length for fish collected in that year.
15

Figure 4. Detections of shortnose suckers on the remote passive integrated transponder (PIT) tag 

antennas in Willow Creek during the spring spawning seasons in 2006–2010. If an individual fish was 

detected more than once in a given season, only the first detection is included. Average daily water 

temperature (°C) was taken from in-stream loggers at the antenna site in 2007, 2008, and 2009.
16

Figure 5. Length frequencies of male and female shortnose suckers captured with trammel nets in Clear 

Lake Reservoir during fall sampling, 2004–2009. Dots on the x-axis in each panel show the median fork 

length for fish collected in that year.
17

Table 1. Catches of Lost River and shortnose suckers in fall trammel net sampling in Clear Lake Reservoir, California, 2006–2009.

[Catches of Klamath largescale suckers and suckers that could not be identified to species are included for completeness. Individuals of unknown sex (Unk) were

excluded from sex ratio calculations (male to female; ♂:♀). The numbers of captured individuals that were tagged in a previous year are given under the year in 

which they were recaptured. Recaptures are a subset of the catches in each year, and include fish tagged in any previous year with any tag type, but exclude 

within-year recaptures]

Year

Lost River suckers Shortnose suckers Klamath largescale suckers Unidentified suckers

♂ ♀ Unk Sex 

ratio ♂ ♀ Unk Sex ratio ♂ ♀ Unk Sex ratio ♂ ♀ Unk Total

2006 148 131 9 1.13 173 318 99 0.54 67 90 22 0.74 11 14 3 1,085

 Recaptures 0 1 0 2 15 2 0 2 0 0 3 0

2007 120 175 3 0.69 254 744 6 0.34 97 193 3 0.50 12 45 1 1,653

 Recaptures 0 2 0 6 37 3 0 2 1 4 17 0

2008 52 73 0 0.71 182 616 3 0.30 37 97 0 0.38 4 24 2 1,090

 Recaptures 1 0 0 10 36 1 0 2 0 1 14 0

2009 136 132 7 1.03 556 1668 32 0.33 15 32 0 0.47 11 24 4 2,617

 Recaptures 6 4 0 18 111 5 0 3 0 7 16 1
18

Table 2. Number of Lost River and shortnose suckers PIT-tagged in fall trammel net sampling and the 

number of individuals detected on remote antennas in Willow Creek during spring spawning migrations, 

2006–2010. 

[Detections are shown by year of tagging (tag cohort). Individual fish can be included in detection counts in multiple 

years. Fish tagged in fall 2005 and fish detected in spring 2006 are included for completeness. Individuals tagged 

prior to fall 2005 with 125 kHz PIT tags could not be detected on the remote antennas in Willow Creek, and those 

fish are excluded from this summary unless they were recaptured and re-tagged with a 134 kHz PIT tag]

Tag cohort Lost River suckers Shortnose suckers

Year detected ♂ ♀ Unk Total ♂ ♀ Unk Total

2005 105 116 1 222 411 1,076 25 1,512

2006 55 32 0 87 214 487 9 710

2007 15 7 0 22 8 38 0 46

2008 49 46 0 95 62 186 5 253

2009 15 3 0 18 5 16 0 21

2010 2 2 1 5 4 18 0 22

2006 148 130 8 286 169 307 96 572

2007 22 4 0 26 12 10 5 27

2008 79 45 4 128 42 93 34 169

2009 15 9 2 26 2 12 0 14

2010 2 1 0 3 3 4 2 9

2007 120 174 3 297 249 708 4 961

2008 65 60 0 125 97 272 1 370

2009 6 10 0 16 3 19 0 22

2010 3 3 0 6 3 19 0 22

2008 52 72 0 124 169 583 2 754

2009 8 7 - 15 4 10 0 14

2010 0 0 - 0 6 24 0 30

2009 130 128 7 265 538 1,555 27 2,120

2010 6 8 0 14 50 122 0 172
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
Hewitt and Hayes—Monitoring of Adult Lost River and Shortnose Suckers in Clear Lake Reservoir, California, 2008–2010—Open-File Report 2013–1301

ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/ofr20131301