Age and Condition of Juvenile Catostomids in 

Clear Lake Reservoir, California

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2013–1188

Age and Condition of Juvenile Catostomids in Clear Lake

Reservoir, California

By Summer M. Burdick, U.S. Geological Survey, and Josh Rasmussen, U.S. Fish and Wildlife Service

Open-File Report 2013-1188

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: 

Burdick, S.M., and Rasmussen, J., 2013, Age and condition of juvenile catostomids in Clear Lake Reservoir, 

California: U.S. Geological Survey Open-File Report 2013–1188, 20 p. 

 

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

the U.S. Government. 

This work was funded by the Ruby Pipeline Corporation and the U.S. Geological Survey and was completed in 

cooperation with the U. S. Fish and Wildlife Service. The findings and conclusions in this article do not necessarily 

represent the views of the U.S. Fish and Wildlife Service. 

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

Description of Study Area .......................................................................................................................................... 4

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

Results....................................................................................................................................................................... 6

Discussion ................................................................................................................................................................. 8

Acknowledgments.................................................................................................................................................... 10

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

Figures 

Figure 1. Map showing sampling locations in Clear Lake, California (Modoc County), 

and its tributaries ..................................................................................................................................................... 13

Figure 2. Boxplots showing standard length of suckers collected in Clear Lake, California (Modoc County) 

by annuli counted on fin rays. Boxplots show the 25th, 50th, and 75th percentile ................................................... 14

Figure 3. Graph showing length frequency for juvenile suckers captured in Clear Lake, California 

(Modoc County) in 2012 .......................................................................................................................................... 15

Figure 4. Graph showing weekly length frequency for juvenile suckers captured in Clear Lake, California 

(Modoc County) in 2012 .......................................................................................................................................... 16

Figure 5. Graph showing standard length in millimeters (mm) and weight in grams (g) of juvenile shortnose 

suckers captured in Clear Lake, California (Modoc County) in 2012 and in Upper Klamath Lake 

(Klamath County) Oregon, from 2006 to 2010......................................................................................................... 17

Tables

Table 1. Number of trap nets set each week in Clear Lake from July 19 to August 15 and from 

September 24 to 26, 2012, using trap nets set overnight. ....................................................................................... 18

Table 2. Weekly catch per unit effort (number of juvenile suckers captured per number of trap nets 

set each week) in Clear Lake from July 19 to August 15 and from September 24 to 26, 2012................................ 18

Table 3. Percentage of agreement in the number of annuli between two structures used to age 

juvenile suckers collected from Clear Lake, California, and its tributaries in 2012................................................... 18

Table 4. Parameter estimates for power curves (that is, weight = a*lengthb) fit to length-weight data 

collected on sacrificed juvenile suckers captured in Clear Lake in 2012, sacrificed juvenile suckers 

captured in Upper Klamath Lake in 2006 and from 2008 to 2010, and with live unidentified juvenile 

suckers captured at the fish evaluation station at the outlet of Upper Klamath Lake in 2012 

(Bureau of Reclamation, unpub. data, 2013) ........................................................................................................... 19

Table 5. Percentage of age-0 and age-1 suckers captured in Clear Lake, California and its 

tributaries in 2012, with afflictions............................................................................................................................ 19
iv

Conversion Factors, Datum, and Abbreviations and Acronyms

Conversion Factors

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch (in. )

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi) 

kilometer (km) 0.54 mile, nautical (nmi) 

meter (m) 1.094 yard (yd) 

Area

hectares (ha) 2.47 acres (ac)

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). 

Abbreviations and Acronyms

Abbreviations Meaning

AFA Aphanizomenon flos-aquae

CPUE catch per unit effort

FL fork length

PIT passive integrated transponder

SL standard length

Reclamation Bureau of Reclamation

USGS U.S. Geological Survey

Wr relative weight
1 

Age and Condition of Juvenile Catostomids in 

Clear Lake Reservoir, California

By Summer M. Burdick, U.S. Geological Survey, and Josh Rasmussen, U.S. Fish and Wildlife

Service

Executive Summary

Although infrequent recruitment of new individuals into the adult spawning 

populations of Lost River suckers (Deltistes luxatus) and shortnose suckers (Chasmistes 

brevirostris) limits recovery of these species in Upper Klamath Lake, it is not clear that 

populations are recruitment limited in Clear Lake Reservoir (hereafter Clear Lake). 

Specifically, some evidence indicates that shortnose suckers may regularly recruit to the 

adult spawning population in Clear Lake. Therefore, a study of early life history patterns 

and recruitment dynamics in Clear Lake may lead to a better understanding of what is 

limiting recovery of suckers in both lakes. Adult suckers in Clear Lake migrate up 

Willow Creek and its tributaries to spawn in some years, but low flow in Willow Creek

may inhibit spawning migrations in other years. It is unclear whether spawning is 

successful, larvae survive, or how frequently juveniles persist to adulthood. 

Environmental variables associated with successful spawning or young-of-year survival 

have not been identified, and early life history for these populations is poorly understood. 

The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, 

initiated a study in 2011 to better understand juvenile sucker life history in Clear Lake, 

and to identify constraints in the early life history that may limit recruitment to the adult 

spawning populations. The relative weights of shortnose suckers from Clear Lake and 

Upper Klamath Lake were compared to examine differences in condition. However, it is 

unclear whether the disparity in relative weights between the populations reflects 

differences in condition, phenotype, or both. Approximately 80 percent of juvenile 

suckers in Clear Lake are shortnose suckers with some morphologic features similar to 

Klamath largescale suckers (Catostomus snyderi), whereas juvenile suckers in Upper 

Klamath Lake can be clearly classified as either shortnose or Lost River suckers. The 

presence of juvenile suckers age-3 and older indicate that production, larval survival, and 

juvenile survival are at least periodically sufficient to lead to recruitment into the adult 

population of shortnose suckers in Clear Lake. 
2 

Introduction

Lost River sucker (Deltistes luxatus) and shortnose sucker (Chasmistes 

brevirostris) are endemic to the Upper Klamath Basin of northern California and southern 

Oregon, where they were both abundant historically. Since the 1920s, several populations 

and spawning subpopulations were extirpated throughout the range of these species 

(National Research Council, 2004). Decreases in Upper Klamath Lake (Klamath County, 

Oregon) populations were noted beginning in the 1960s, eventually leading to their 

federal listing as endangered in 1988 under the Endangered Species Act of 1973, as 

amended (U.S. Fish and Wildlife Service, 1988). Clear Lake (Modoc County, California), 

Upper Klamath Lake, and the tributaries of both lakes are designated as critical habitat 

for Lost River and shortnose suckers (U.S. Fish and Wildlife Service, 2012, 2013). 

Poor recruitment into adult spawning populations is one of several reasons cited 

for the continued decline and lack of recovery in Upper Klamath Lake sucker populations 

(National Research Council, 2004). It is not clear, however, whether these species are 

recruitment limited in Clear Lake, particularly the shortnose sucker (D.A. Hewitt and 

E.C. Janney, U.S. Geological Survey [USGS], written commun., 2011). Consistently high 

mortality, relative to natural levels, at approximately 5–7 months of age (August–

October) is thought to lead to poor recruitment into Upper Klamath Lake adult sucker 

populations (Burdick and others, 2009). A 1995 cohort of suckers (species unknown) in 

Clear Lake continued to be detectable a year later in 1996, indicating that these fish 

survived longer than is typical in Upper Klamath Lake (U.S. Geological Survey, unpub. 

data, 1996). It is not clear from the limited data collected, however, if first year survival 

is typical, or if the 1995 cohort is an anomaly. 

Apparent cohorts of smaller Lost River suckers (about 300–400 mm fork length 

(FL)) were evident in annual autumn sampling in Clear Lake from 2005 to 2008, but 

these fish did not appear to survive in subsequent years (D.A. Hewitt and E.C. Janney, 

U.S. Geological Survey, written commun., 2011). Length frequency data indicate

somewhat regular recruitment of shortnose suckers to the adult spawning population, 

based on a broad distribution of lengths in the captured individuals greater than 300 mm 

FL. However, length is a relatively poor surrogate for age of shortnose suckers in Clear 

Lake, which causes uncertainty about the interpretation of length-frequency plots for this 

species (D.A. Hewitt and E.C. Janney, U.S. Geological Survey, written commun., 2011). 

The Klamath largescale sucker (Catostomus snyderi) also occurs in Clear Lake 

and its tributaries and is believed to hybridize with the shortnose sucker. The identity of 

shortnose-like suckers in Clear Lake has been debated at least three times in the scientific 

literature since the late 1800s (summarized in Koch and others, 1975), and was most 

recently examined by Markle and others (2005). Markle and others (2005) concluded that 

(1) shortnose and Klamath largescale suckers exist in Clear Lake, (2) the two species are 

more similar in Clear Lake than in other parts of their range, and (3) the two species are 

difficult to distinguish as juveniles. The latter is confirmed by USGS passive integrated 

transponder (PIT) tag data, in which fish tagged at less than 350 mm standard length (SL) 

were sometimes identified as Klamath largescale suckers when tagged, and as shortnose 

suckers when recaptured a year or two later (U.S. Geological Survey, unpub. data, 2011). 
3 

Using the characteristics described by Markle and others (2005), USGS crews identified 

about 59 percent of adult suckers captured in autumn trammel net sampling as shortnose 

suckers, and only18 percent as Klamath largescale suckers (Barry and others, 2009). 

However, no quantitative/objective methods of distinguishing the species currently exist, 

and identifications are largely based on subjective assessment of nuanced morphological 

character traits.

A combination of PIT tag and telemetry data are useful for describing the 

spawning runs of Lost River and shortnose suckers from Clear Lake. Both species initiate 

spawning runs up Willow Creek on the ascending limb of the hydrograph at water 

temperatures between 5 and 6 °C, which typically occur in late February or early March 

(Barry and others, 2009). Telemetry data collected in 2011 indicate that Willow Creek 

and its major tributary Boles Creek were the only locations that Clear Lake suckers 

spawn (U.S. Geological Survey, unpub. data, 2011). The magnitude and duration of 

spawning runs are larger in years with high Willow Creek discharge (Barry and others, 

2009). Low flow in Willow Creek appears to severely limit spawning migrations in some 

years (Barry and others, 2009). However, the precise nature of the relation between 

discharge and the number of fish that ascend Willow Creek to spawn is unknown because 

there is no flow gage in Willow Creek. Furthermore, it is unclear if suckers forgo 

spawning in years of low flow, or if they spawn in an alternative location. Telemetry data 

indicate that Lost River suckers are restricted to the mainstem of Willow Creek, whereas 

shortnose suckers travel up smaller tributaries to Willow Creek (U.S. Geological Survey, 

unpub. data, 2011). Spawning migrations appear to cease when Willow Creek water 

temperatures reach 10 °C, which typically occurs in mid-April (Barry and others, 2009). 

Less is known about the early life history of suckers in Clear Lake than about 

their spawning migrations. In 1993, Lost River suckers out-migrated as larvae from April 

18 to June 1 and shortnose suckers out-migrated as both larvae and juveniles from April 

20 until late July (Scoppettone and others, 1995). Diurnal samples were not collected for 

comparison, but nocturnal migration behavior is consistent with out-migrating larvae in 

the Williamson River, a tributary to Upper Klamath Lake (Cooperman and Markle, 

2003). Basic data such as water temperature and stream flow data for Willow Creek are

lacking from 1993, and larval catch data are only available for a single year, so it is 

impossible to tell if the out-migration of larvae is related to these environmental 

variables. Collection of juvenile and adult suckers from Willow Creek at the Forest 

Service Road 48N08 crossing in August 1995 suggests that a resident or fluvial life 

history form may be using this tributary to Clear Lake (Perkins and Scoppettone, 1996). 

However, Perkins and Scoppettone (1996) did not record the species of sucker they 

observed. Given that Klamath largescale suckers occupy the system and are known to be 

fluvial, it is possible that the captured fish were not one of the endangered suckers. 

There are two goals for the research reported on in this document: (1) better 

understand juvenile sucker life history in Clear Lake and (2) identify constraints if any in 

the early life history that may be limiting recruitment to the adult spawning populations 

in Clear Lake. 
4 

Description of Study Area

Clear Lake was historically a natural lake covering about 6,500 ha with an 

associated marshy area to the east through which the main tributary (Willow Creek) 

flowed. This marshy area was permanently inundated, expanding the lake by about 3,900 

ha, in 1910 when the Bureau of Reclamation built a dam on the Lost River near its outlet

producing a coterminous water body with western and eastern lobes (Buettner and 

Scoppettone, 1991). The Clear Lake watershed is arid high desert and is almost entirely

publicly owned. The lake itself is owned by the U.S. Fish and Wildlife Service’s Clear 

Lake National Wildlife Refuge (established in 1911), but the upper watershed is part of 

the U.S. Forest Service’s Modoc National Forest. The area immediately surrounding 

Clear Lake is rocky with sagebrush (Artemesia spp.) steppe plant communities and 

western juniper (Juniperus occidentalis), although the upper watershed is populated with 

ponderosa pine (Pinus ponderosa) (Buettner and Scoppettone, 1991). Water depth in the 

western lobe of the lake can be as deep as 4 m but is less than 2 m deep in the eastern 

lobe at full pool. Substrate consists mostly of sand and fines, with lava rock boulders 

scattered throughout the lake. Clear Lake is very turbid, which is likely the result of wind 

coupled with shallow water. These conditions appear to prevent the large-scale algae 

blooms that occur annually on Upper Klamath Lake. The most apparent species of algae

in Clear Lake is the presumably non-toxic Aphanizomenon flos-aquae (AFA). A bloom 

of a potentially toxin producing Microcystis sp. was reported by Buettner and

Scoppettone (1991) in July 1989, but it is unclear if the algal species was correctly 

identified. 

Two creeks in the basin provide spawning habitat for suckers. Willow Creek, the 

main tributary to Clear Lake, is a perennial stream that enters at the northwestern shore 

near the dam. Boles Creek joins Willow Creek less than 1 km upstream of Clear Lake 

and is a low gradient intermittent stream. Downstream of Boles Creek, Willow Creek is 

“very wide with large boulders interspersed with cobble and gravel,” and upstream of 

Boles Creek, Willow Creek is “steep and narrow with fine to coarse gravels and 

occasional reaches of solid lava rock” (Buettner and Scoppettone, 1991). There are 

numerous small earthen dams that create small stock ponds in Willow and Boles Creeks. 

The status of these dams as migration barriers to suckers is presently unknown. Spawning 

is known to occur in Willow and Boles Creeks, but has not been documented in Mowitz 

Creek, a small intermittent stream that enters Clear Lake at the southern end of the 

eastern lobe. 

Methods

Suckers were sampled using trap nets in Clear Lake between July 19 and August 

15 and again between September 24 and 26, 2012. Samples sites were located in one of 

three areas along shorelines in the western lobe of the lake (fig. 1) based on knowledge of 

juvenile sucker distribution from previous efforts (Burdick and Rasmussen, 2012). The 

numbers of nets set in each shoreline area range from 0 to 15, and are given by week in 

table 1. Two additional sample sites were located in Boles Creek and one additional site 

was located in Willow Creek near the mouth of Mammoth Springs (fig. 1). Trap nets 

were rectangular with mouth dimensions of 0.609 × 0.914 m, a 10-m lead, and three 

internal fykes. These nets were green with 6.4-mm mesh, nylon netting. Nets were set 
5 

between 0739 and 1533 hours and pulled the next day between 0750 and 1529 hours for a 

target soak time of 20 hours. A backpack mounted electrofishing unit was used to sample 

suckers in Boles Creek. Four electrofishing surveys, lasting between 20 and 75 minutes 

each, were completed. A survey was conducted both upstream and downstream of Modoc 

County Road 136 and upstream and downstream of the Forest Service Road 46 crossings 

with Boles Creek. 

Parasites that could be observed without magnification, SL, FL, deformities, or 

any afflictions or abnormalities were recorded for each sucker. Approximately one-third 

of untagged suckers less than 100 mm SL were sacrificed by an overdose of MS-222 then

preserved in buffered formalin. Sacrificed suckers were identified to species using 

methods described by Markle and others (2005), which involves counting vertebrae and 

gill rakers, and examining lip morphology. Anatomy was imaged using a mammography 

machine to obtain vertebral counts. Sacrificed suckers were weighed to the nearest tenth 

of a gram and lapillus otoliths and opercles were removed for aging. Following the 

examples of Koch and others (1975) and Buettner and Scoppettone (1991), but in contrast 

to Andreasen (1975), we refer to fish that have characteristics of shortnose and Klamath 

largescale suckers from Clear Lake as shortnose suckers rather than Klamath largescale 

suckers or hybrids. 

Captured suckers were either PIT tagged or a fin ray was removed. This was done 

to limit the amount of stress inflicted on the animal to a single invasive procedure (that is, 

tagging or fin clipping). Suckers equal to or greater than 70 mm SL were given a PIT tag 

and released alive at the site of capture when water temperatures were less than 20 °C 

(Burdick, 2011). Complete pectoral fin rays were removed for aging by cutting as close 

to the fin base as possible. Sections were taken from the proximal end of the fin ray and 

read under transmitted light at 5–10× magnification. 

Fin rays from all suckers and all three calcified structures from sacrificed suckers 

were examined to estimate age. Fin rays were mounted in epoxy, sectioned, and viewed 

by two technicians under magnification using transmitted light to estimate age. The 

number of annuli was first determined in blind reads, with each technician having no 

knowledge of the other’s total annuli count. When there was a discrepancy in the number 

of annuli, technicians examined fin rays together and came to a consensus about the 

estimated age of each fish. Flesh was removed from opercles and structures were 

examined without preparation using transmitted light. Lapillus otoliths were mounted on 

glass slides, sanded to the core, flipped and sanded again until annuli could be clearly 

counted. A single technician read all opercles and otoliths. 

We compared the slope of the length weight relation between sacrificed juvenile 

shortnose suckers captured in Clear Lake in 2012 with sacrificed juvenile shortnose 

suckers captured in Upper Klamath Lake in 2006 and from 2008 to 2010, and with live 

caught unidentified juvenile suckers captured at the fish evaluation station at the outlet of 

Upper Klamath Lake in 2012 (Bureau of Reclamation, unpub. data, 2013). Due to wind 

and wave action, in-field weight data collected for fish from Clear Lake in 2011 

were inaccurate. Therefore we did not compare weight data between Clear Lake suckers 

collected in 2011 and 2012. Linear models were fit to log transformed length and weight 

data and slopes were compared using ANOVA in program R (R Core Team 2012). Power 

curves (that is, Weight = Constant * lengthslope) were fit to data from each year using the 
6 

nlsLM function in program R for display and reporting purposes and parameter estimates 

and their 95 percent confidence intervals are reported. 

The relative weight (Wr) of sacrificed shortnose suckers captured in Clear Lake in 

2012 was calculated as the weight for each individual divided by the predicted weight for 

its SL, based on a length-weight relationship estimated from 1,013 juvenile shortnose 

suckers captured in Upper Klamath Lake from 2006 to 2010 (Burdick and others, 2007; 

U.S. Geological Survey, unpub. data, 2010), and multiplied by 100 (Anderson and 

Neumann, 1996). Therefore Wr is scaled around 100, such that values less than 100 

indicate relatively poor condition, and individuals with values greater than 100 are in 

relatively good condition, as compared to the expected weights of Upper Klamath Lake 

juvenile suckers of the same length.

Results

Trap net catch per unit effort (CPUE) ranged from 0.6 to 4.3 suckers per set in 

Clear Lake (table 2). Only one juvenile sucker was captured in 16 nets set in Willow 

Creek and no suckers were captured in 12 nets set in Boles Creek. A single 244 mm SL 

Klamath largescale sucker was captured using electrofishing in Boles Creek downstream 

of Forest Service Road 46. Juvenile sucker catch rates were slightly greater in most 

weeks on the South Shore compared to the West Shore and Bird Inlet (table 2). 

A total of 72 juvenile suckers were sacrificed, 11 were found dead in our nets, and 

3 died during handling. All of these fish were examined for species specific 

characteristics (that is, number of vertebrae, number of gill rakers, and lip morphology). 

Of these fish, 70 (81.4 percent) were identified as shortnose suckers, 9 (10.5 percent) 

were identified as Lost River suckers, and 7 (8.1 percent) had characteristics intermediate

of shortnose, Lost River, and Klamath largescale suckers. 

A total of 42 juvenile suckers (standard length 72–285 mm) were given 12 mm 

PIT tags. Four (9.5 percent) of the tags from these fish were redetected in 2012 on 

piscivorous bird colonies in the Clear Lake National Wildlife Refuge. Tags from two 

juvenile suckers tagged in 2011 also were detected in 2012. One of these, tagged in the 

western lobe of Clear Lake, was detected on a bird colony in the eastern lobe of Clear 

Lake. The other was recaptured on September 19, 2012, approximately 1.9 km north of 

where it was tagged on June 28, 2011. 

The agreement in estimated ages between any two aging structures taken from 

sacrificed fish, all less than 100 mm SL, was at best 50 percent (table 3). When age 

estimates were compared between two structures, the vast majority (range was between 

91 and 96 percent) were only different by 1 year. Opercles were most commonly 

assigned an age of 0, whereas fin rays were most commonly assigned an age of 1 and 

otoliths were about equally as likely to be assigned the age of 0 or 1. Annuli were most 

clearly identified on fin rays and length frequency data mostly supported fin ray 

estimated ages for the two youngest age classes (fig. 2). Age-2 and age-3 fish appeared to 

be indistinguishable based on length. Age-4 and age-5 suckers appeared to fall into 

distinct length bins, but our sample only contained seven fish with fin ray estimated ages 

in this range making conclusions about age and length relations tenuous (fig. 2). We used 

fin ray estimated ages in the rest of our analysis, based on length frequency and fin ray 

agreement, the clarity of annuli on fin rays, and the concern that formalin may have 

degraded opercles and otoliths. 
7 

The number of annuli counted on fin rays ranged from 0 to 6. Of the 384 juvenile 

suckers aged using fin rays, 17 percent were age-0, 61 percent were age-1, 17 percent 

were age-2, 3 percent were age-3, and the remainder were age-4 to age-6. Of the 69 

shortnose suckers that were sacrificed and aged with fin rays, 30 percent were estimated 

to be age-0, 58 percent were estimated to be age-1, and only 12 percent were estimated to 

be age-2. Standard length but not age data were collected for 59 suckers because they 

were tagged and released or the quality of the fin ray was insufficient to obtain an age 

estimate. The length frequency of un-aged fish was similar to those that were aged, 

indicating that aged fish were representative of all captured suckers (fig. 3). 

Age-0 suckers appeared to grow faster than age-1 suckers. The median standard 

length of age-0 suckers increased by an average of 7.8 mm per week from the week of 

July 22 to the week of August 5. The median age-0 standard length then decreased during 

the week of August 12. In contrast, the median standard length of suckers with fin ray 

estimated ages of 1 increased by an average of 3.2 mm per week from the week of July 

22 to the week of August 12. This resulted in overlapping length frequency distributions 

for these age classes by the week of July 29 (fig. 4). Too few suckers were identified as 

Lost River suckers to determine differences in growth among species. 

Juvenile shortnose suckers captured in Clear Lake in 2012 (n=84) weighed less

given their length than juvenile shortnose suckers captured in Upper Klamath Lake 

between 2006 and 2010 (n=1,013) and juvenile suckers that were not identified to species 

at the fish evaluation station in 2012 (n=466; p<0.001) (Bureau of Reclamation, unpub. 

data, 2013)(table 4; fig. 5). This was particularly true for the smallest suckers. However, 

power curves fit to length-weight data indicate that Clear Lake shortnose suckers gained 

weight more rapidly in proportion to their length when compared to suckers from Upper 

Klamath Lake (table 4; fig. 5), that is, the estimated slope or exponent is greater. When 

compared to Upper Klamath Lake shortnose suckers captured from 2006 to 2010, only 1 

of 70 sacrificed juvenile shortnose suckers captured in Clear Lake in 2012 had a relative 

weight greater than 100. This was the only fish that weighed more given its length than 

an average fish of a similar length collected in Upper Klamath Lake prior to 2011. 

With the exception of parasitic infections by adult female anchor worms, juvenile 

suckers captured in Clear Lake in 2012 had few afflictions (table 5). Twenty-eight 

percent of age-0 and 36 percent of age-1 suckers were parasitized by at least one adult 

female anchor worm (Lernaea cyprinacea), but none had more than three anchor worms. 

Four percent of age-0 suckers and 12 percent of age-1 suckers had skin abrasions or other 

infectious wounds. Other afflictions such as bulging, missing, or foggy eyes, split or 

damaged fins, opercle deformities, and parasites other than anchor worms were 

uncommon for juvenile suckers from Clear Lake in 2012 (table 5). 
8 

Discussion

The species composition of juvenile suckers captured in trap nets was similar to 

adult suckers captured in trammel net surveys, indicating that shortnose suckers are the 

dominant sucker species in Clear Lake, with Lost River suckers being much less 

common. Shortnose suckers made up 81 percent of sacrificed juvenile suckers collected 

from Clear Lake in 2012 and 78 percent in 2011 (Burdick and Rasmussen, 2012). Adult 

suckers captured in Clear Lake in 2011 and 2012 are composed of about 81 percent 

shortnose suckers and 16 percent Lost River suckers (U.S. Geological Survey, unpub. 

data, 2012). Lost River suckers made up 8 percent of sacrificed juvenile suckers in 2012 

but were not detected at all in 2011. The lack of Lost River suckers in 2011 probably is 

the result of their rarity and the small sample size of fish sacrificed for species 

identification. 

Although the lack of agreement in the number of annuli found on age structures 

indicates poor precision of age estimates, age estimates from fin rays do not appear to be 

biased. The high number of opercles with no annuli may be due to preservation in 

formalin. Formalin tends to degrade calcified structures and may have had a more direct 

effect on opercles that are located closer to the exterior of the body compared to otoliths 

that were protected by the skull or fin rays that were removed prior to fish preservation 

(G. Scoppettone, U.S. Geological Survey, oral commun., 2013). The annuli clarity on fin 

rays was much better than on opercles or otoliths. Additionally, a comparison between 

length frequency data and fin ray ages indicates that estimated ages based on fin rays are 

relatively unbiased. Due to some overlap in lengths among age classes, particularly in 

August samples, length is an unreliable indicator of sucker age. Because of the suspected 

lack of precision in fin ray age data, these data are useful for descriptions of age 

distribution but are inappropriate for examining effects on specific cohorts or estimating 

mortality rates. 

Juvenile sucker catches in 2012 were comprised predominantly of age-1 fish. This 

is most likely due to more favorable spawning conditions (that is, higher flows) in 

Willow Creek in 2011 compared to 2012. This is evidenced by the much greater number 

of PIT tagged adult suckers detected ascending Willow Creek during annual spawning 

migration monitoring in 2011 (3,147) than in 2012 (604; U.S. Geological Survey, unpub. 

data, 2013). Other potential explanations for higher catches of age-1 compared to age-0 

suckers include delayed recruitment of age-0 suckers into sampling gear or into the 

sampled habitats. We commonly capture age-0 suckers less than 40 mm SL using trap 

nets in Upper Klamath Lake, therefore it is unlikely that the gear limited catches of small 

suckers in Clear Lake (Bottcher and Burdick, 2010). Because trap net sampling was 

restricted to the western lobe of Clear Lake and spawning occurs in tributaries that enter 

the eastern lobe, it is possible that suckers were not fully dispersed into the sampled area 

until they were a year old. However, in 2011 catches of age-0 suckers were four times 

that of age-1 suckers indicating that age-0 catches were not limited by dispersal into the 

western lobe but rather reflected the substantial production in 2011 and very low 

production in 2010 (Burdick and Rasmussen, 2012). 

The lack of captures of larger and older individuals indicate that age-1 and older 

suckers in Clear Lake experienced mortality, reduced selectivity as they aged, or a 

combination of both. Reduced selectivity for suckers approximately 300 to 400 mm FL is 

confirmed by the presence of these individuals in annual trammel net sampling that 
9 

targets adult suckers (U.S. Geological Survey, unpub. data, 2013). Because age specific 

selectivity and mortality are confounded, there is variability in annual production, and 

uncertainty in age estimates, the rate of mortality cannot be estimated from these data

using traditional catch curve methods. In both Clear and Upper Klamath Lakes, the 

decrease in catch rates of age-1 and age-3 suckers indicate mortality is on the same order 

of magnitude but, more age-3 and older juvenile suckers were captured in Clear Lake 

than in Upper Klamath Lake. In Clear Lake, 17 juvenile suckers estimated to be age-3 or 

older based on fin rays and length were captured in 2012 for a catch rate of 0.083 suckers 

per net. Whereas, only 4 juvenile suckers estimated to be age-3 or older based on length 

were captured from 2007 to 2009 in Upper Klamath Lake for a catch rate of 0.001 

suckers per net (U.S. Geological Survey, unpub. data, 2013). The number of older 

juvenile suckers captured in Clear Lake may indicate production, larval survival, youngof-year survival or a combination of these factors are better in Clear Lake than in Upper 

Klamath Lake. 

It is unclear whether the disparity in relative weights among the groups we 

examined reflects differences in condition, phenotype, or both. Shortnose suckers in 

Clear Lake generally exhibit external morphological characteristics intermediate to 

shortnose suckers and Klamath largescale suckers in Upper Klamath Lake (Markle and 

others, 2005). The fact that juvenile shortnose suckers in Clear Lake apparently weigh 

less at any given length than similar individuals in Upper Klamath Lake may be further 

evidence of these phenotypical differences. Given that individuals from Clear Lake did 

not exhibit any clear signs of poor condition, it is likely these differences are due to some 

phenotypic reason, whether genetic or environmental. 

Age-0 and age-1 suckers were parasitized by female anchor worms in both Clear 

and Upper Klamath Lakes, but the number of anchor worms per fish was not a cause for 

concern in either lake. Twenty-eight percent of age-0 and 36 percent of age-1 suckers 

captured in Clear Lake in 2012 were parasitized by at least one adult female anchor 

worm. Rates of anchor worm parasitism were lower in Clear Lake in 2011 when 16 

percent of age-0 suckers and two of five age-1 suckers had anchor worms. The annual 

rate of anchor worm infection was no greater than 18 percent on putative age-0 suckers 

and was between 20 and 50 percent on putative age-1 suckers collected from Upper 

Klamath Lake between 2008 and 2010 (Burdick and others, 2009; Bottcher and Burdick, 

2010; Burdick and VanderKooi, 2010; Burdick, 2012). Juvenile suckers from Clear Lake 

had no more than three anchor worms per infected fish. The vast majority of parasitized 

age-0 and about one-third of parasitized age-1 suckers examined from Upper Klamath 

Lake from 2008 to 2010 had only one anchor worm attached, but as many as 18 anchor 

worms have been recorded on an age-1 sucker from Upper Klamath Lake (Burdick, 

2012). The prevalence and intensity of anchor worm parasitism may not be cause for 

alarm (Robinson and others, 1998). Some evidence suggests that anchor worm infections 

on their own do not pose serious threats to overall fish health (Robinson and others, 

1998). However, secondary infection may occur where anchor worms attach to the fish 

(Robinson and others, 1998). 
10

Deformed opercles were somewhat common on juvenile suckers captured in 

Upper Klamath Lake from 2008 to 2010 but were only detected on one age-0 and one 

age-1 sucker collected from Clear Lake in 2012 and on 3 percent of juvenile suckers from 

Clear Lake in 2011. In Upper Klamath Lake, up to 18 percent of putative age-0 and up to 

9 percent of putative age-1 suckers have short or malformed opercles (Burdick and 

others, 2009; Bottcher and Burdick, 2010; Burdick and VanderKooi, 2010; Burdick, 

2012). The frequency of deformed opercles in Clear Lake is more consistent with rates of 

this deformity observed in the early 1990s in Upper Klamath Lake, when 4.7 percent of 

Lost River suckers and 1.4–3.1 percent of shortnose suckers exhibited opercle 

deformities (Plunkett and Snyder-Conn, U.S. Fish and Wildlife Service, written 

commun., 2000). It is important to determine why opercle deformities are different 

among the two lakes because they have been shown to lower resistance to oxygen stress 

and predispose fish to infections by bacteria, parasites, and fungi (Galeotti and others, 

2000; Beraldo and others, 2003). Although these deformities are common in hatchery 

raised fish and considered non-lethal, deformed opercles in combination with extended 

periods of low dissolved oxygen concentrations and abundant parasites may be lethal 

combination for age-0 suckers in Upper Klamath Lake. 

In summary, the sucker community in Clear Lake is dominated by shortnose 

sucker, but both federally listed species do produce viable young each year. Production is 

apparently variable from year to year, but our efforts here are not able to quantify the 

juvenile survival and subsequent recruitment rates to the adult populations in Clear Lake. 

Juveniles of shortnose sucker tend to be heavier at a given length in Upper Klamath Lake, 

compared to Clear Lake; they also have higher rates of opercle deformities but similar 

rates of parasitism. These differences may provide clues about the cause of limited 

recruitment to the adult spawning populations, but we did not identify specific 

constraints. Continued comparisons of ecology and life history between these two 

populations of these species will be very useful in furthering our understanding of the 

problems facing each population. 

Acknowledgments

This project was funded by Ruby Pipeline L.L.C. Corporation (El Paso, Tex.). 

Data were collected with the help of Amari Dolan-Caret, Elizabeth Ng, Travis Ciotti, 

Raefield Benson, and Jesse Kane (all of the U.S. Geological Survey). Alta Harris and 

Amari Dolan-Caret (both of the U.S. Geological Survey) developed and manage the 

database used in this research. 
11

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Iwanowicz, D., 2009, Distribution, health, and development of larval and juvenile Lost 

River and shortnose suckers in the Williamson River Delta restoration project and 

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Open-File Report 2009–1287, 76 p. (Also available at 

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sucker investigations in Clear Lake, California—2011 pilot study summary: U.S. 

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variables in Upper Klamath Lake, Oregon—2008 annual data summary: U. S. 

Geological Survey Open-File Report 2010–1051, 36 p. (Also available at 

http://pubs.usgs.gov/of/2010/1051/.) 
12

Burdick, S.M., Wilkens, A.X., and VanderKooi, S.P., 2007, Near-shore and off-shore 

habitat use by endangered, juvenile Lost River and shortnose suckers in Upper Klamath 

Lake, Oregon—2006 data summary: U.S. Geological Survey Open-File Report 2007–

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of the American Fisheries Society, v. 132, p. 1,138–1,153. 

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13

Figure 1. Map showing sampling locations in Clear Lake Reservoir, California (Modoc County), 

and its tributaries. The lake was sampled from July 19 to August 15 and from September 24 to 26, 

2012, using trap nets set overnight. Electrofishing and trap netting also were conducted at the 

Modoc County Road 136 and Forest Service Road 46 crossings with Boles Creek. 
14

Figure 2. Boxplots showing standard length of suckers collected in Clear Lake, California (Modoc 

County) by annuli counted on fin rays. Boxplots show the 25th, 50th, and 75th percentiles. 

Whiskers indicate the 10th and 90th percentiles and dots indicate outliers. The sample sizes used 

to create each box are given along the x-axis. 
15

Figure 3. Graph showing length frequency for juvenile suckers captured in Clear Lake, California 

(Modoc County) in 2012. Suckers that were aged using fin rays are shown in white and those that 

were not aged are shown in black. 
16

Figure 4. Graph showing weekly length frequency for juvenile suckers captured in Clear Lake, 

California (Modoc County) in 2012. The numbers of suckers captured each week are given in each 

panel. The median weekly length for age-0 suckers is shown with a black dot and for age-1 

suckers with a black triangle. 
17

Figure 5. Graph showing standard length in millimeters (mm) and weight in grams (g) of juvenile 

shortnose suckers captured in Clear Lake, California (Modoc County) in 2012 and in Upper 

Klamath Lake (Klamath County) Oregon, from 2006 to 2010. Data also are shown for unidentified 

suckers captured in the Fish Evaluation Station near the outlet of Upper Klamath Lake in 2012 

(Bureau of Reclamation, unpub. data, 2012). A fitted power curve (that is, Weight = 

Constant*LengthSlope) is shown for suckers captured in Clear Lake (solid), Upper Klamath Lake 

(dotted), and the Fish Evaluation Station at the outlet of Upper Klamath Lake (dashed). Confidence 

intervals for these curves are provided in table 4.
18

Table 1. Number of trap nets set each week in Clear Lake from July 19 to August 15 and from 

September 24 to 26, 2012, using trap nets set overnight. 

[Sampling locations are shown in figure 1]

Week

Area July 16 July 23 July 30 Aug 6 Aug 13 Sept 24

Bird Inlet 5 15 15 15 15 0

South Shore 5 15 15 15 15 4

West Shore 5 15 15 15 15 6

Total 205

Table 2. Weekly catch per unit effort (number of juvenile suckers captured per number of trap nets 

set each week) in Clear Lake from July 19 to August 15 and from September 24 to 26, 2012. 

[Sampling locations are shown in figure 1]

Week

Area July 16 July 23 July 30 Aug 6 Aug 13 Sept 24

Bird Inlet 0. 8 1. 6 1. 1 0. 7 1. 3 NA

South Shore 2. 0 2. 1 2. 9 3. 8 4. 3 3. 3

West Shore 0. 6 2. 1 3. 7 1. 4 2. 1 1. 5

Total 2.2

Table 3. Percentage of agreement in the number of annuli between two structures used to age 

juvenile suckers collected from Clear Lake, California, and its tributaries in 2012. 

[Totals of 64 shortnose suckers and 14 suckers identified as either Lost River suckers or as suckers having 

characteristics intermediate of shortnose, Lost River, and Klamath largescale suckers were examined in the 

age analysis] 

Percentage of agreement

Structures Shortnose suckers Other suckers

Opercles-Fin Rays 42 43

Otoliths - Fin Rays 30 43

Opercles - Otoliths 33 50
19

Table 4. Parameter estimates for power curves (that is, weight = a*lengthb) fit to length-weight data 

collected on sacrificed juvenile suckers captured in Clear Lake in 2012, sacrificed juvenile suckers 

captured in Upper Klamath Lake in 2006 and from 2008 to 2010, and with live caught unidentified 

juvenile suckers captured at the fish evaluation station at the outlet of Upper Klamath Lake in 2012 

(Bureau of Reclamation, unpub. data, 2013).

Area a

95-percent confidence 

Interval b

95-percent

confidence Interval

Clear Lake 3.66E-06 (2.05e-6 - 6.52e-6) 3.24 (3.12 - 3.36)

Upper Klamath Lake 1.45E-05 (1.32e-5 - 1.60e-5) 3.02 (3.00 - 3.04)

Fish Evaluation Station 1.71E-05 (1.31e-5 - 2.21e-5) 2.97 (2.91 - 3.02)

Table 5. Percentage of age-0 and age-1 suckers with afflictions captured in Clear Lake, California 

and its tributaries in 2012. 

[Ages of suckers are based on the number of annuli counted on fin-ray sections] 

Affliction

Age-0

(percent)

Age-1

(percent)

Eyes bulging or missing 0 1

Damaged fins 0 2

Abrasions 4 12

Deformed opercles <1 <1

Anchor worms 28 36

Lamprey 1 3

Other parasite 1 0

None 65 50
20

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Burdick and Rasmussen— Age and Condition of Juvenile Catostomids in Clear Lake Reservoir, California—Open-File Report 2013–1188