Sample Design

Suckers were sampled with trap nets to assess species-specific annual variability in production and growth, as well as annual and seasonal variability in survival of juvenile suckers in Upper Klamath and Clear Lakes. The timing of the sampling periods was selected based on previous catch data in Upper Klamath Lake. Specifically, we targeted age-1 suckers in early June, the start of age-0 sucker catches in July, the peak of age-0 sucker catches in August, and the tail end of age-0 sucker catches in September (Burdick and Martin, 2017). In 2015, sampling was conducted over three 3-week periods simultaneously in Upper Klamath and Clear Lakes. An evaluation of the study design in 2015 indicated that with increased effort concentrated into shorter time periods growth and differences in catch rates between sampling periods could be better described. Starting in 2016, sampling was conducted during 1 week in each month with weekly sampling alternated between lakes within each sampling month. A July sampling period was added in 2018 to capture early age-0 suckers. Sampling occurred in the same calendar weeks each year within each lake, with the exception of July 2018. Poor air quality resulting from wildfires limited access to Upper Klamath Lake and delayed the sampling effort by 1 week when compared to previous years.

The catch data in this report is only relevant to suckers from about 45 to 300 millimeters (mm) standard length (SL) based on the trap net selectivity. Small age-0 suckers (<45 mm SL) have a low catchability in trap nets (Burdick and Martin, 2017). Because adult suckers (>300 mm SL) are captured at high rates in spring and fall trammel net sampling and infrequently in summer trap net sampling, we presume trap nets select for smaller suckers relative to trammel nets (Hewitt and Hayes, 2013).

Fixed sampled sites were selected in a variety of habitats throughout both lakes to reduce potential sample bias caused by spatial heterogeneity in the densities, species, ages, size or health of suckers. Age-0 suckers greater than 45 mm SL are homogenously distributed by species and size within Upper Klamath Lake (Hendrixson and others, 2007; Burdick and Hewitt, 2012). However, age-1 suckers are more likely to be found in shallow (<1 m deep) near-shore habitats in the spring and deep water (about 2 m) in the summer (Bottcher and Burdick, 2010). Spatial patterns among age-classes of suckers have not been identified in Clear Lake (Burdick and Rasmussen, 2012). Sample areas were either 1-kilometer long sections of shoreline or 300 square meters (m²) offshore areas. Within each area, 10 fixed sites were identified as accessible given a variety of water levels. In 2021 and 2022, as in past years, we attempted to set nets at 8 sites at each area in Upper Klamath Lake and 7 sites at each area in Clear Lake during each sampling period (tables 1 and 2). However, because of low water levels in 2021, only one established site at the Tulana area in Upper Klamath Lake was sampled in June, July, and August. Supplemental sites were sampled at the mouth of the Tulana wetlands in July and August of 2021. In September of 2021, neither the established site nor the supplemental sites were accessible for the Tulana area. In Clear Lake, the dam channel area was only accessible in June and was not sampled in July, August, or September because of low water levels. Furthermore, in 2022 only three of the sites at the dam channel were set. To address the concern of catches at fixed sites not being reflective of the sucker population, random sites were sampled during all sample years. Previous work has found no significant difference between fixed verses random sites (Burdick and others, 2016). In order to compare catches between years, only fixed sites are reported in this publication.

Sample locations were adjusted for water depth each year. Sites that were shallow and near shore in low water years of 2015 and 2016 were often in more than 3 m of water and far from shore from 2017 to 2020. Because juvenile sucker catch rates with trap nets decrease at depths greater than 3 m (Burdick and Hewitt, 2012), few juvenile suckers were captured at this depth. We adjusted sample locations by going to the 2015 and 2016 locations, then driving directly toward shore from the original site until we were in less than 3 m of water before setting the trap nets. In 2021 and 2022 sampling sites, the 2015 and 2016 locations were too shallow to set nets. Therefore, the crews attempted to go to the preset locations, but set the nets further from shore before they reached the preset location.

Fish Handling and Sampling

Sampling was conducted with rectangular trap nets with mouth dimensions of 0.61 × 0.91 m, a 10-m-lead, and 3 internal fykes. Standard length and fork length were recorded for each captured individual. The leading left pectoral fin ray was removed at the proximal joint for aging. Fin rays were not collected from small suckers (35–60 mm SL) from Upper Klamath Lake since they were presumed to be age-0 fish based on length at date of capture (Burdick and Martin, 2017). We compared the length and number of annuli on fish with fin rays collected to length of suckers without fin rays collected to validate our length-based age assumptions. A small (about 2 square millimeters [mm²]) piece of tissue from the caudal fin was collected for genetic identification to species. All collected suckers were measured, aged either by fin ray or presumed age-0, and identified to species via genetic analysis. The exception being three suckers captured during 2021 and four suckers captured during 2022 in Clear Lake, that had either missing genetics and or missing ages. Emaciation, deformities, macro parasites, petechial skin hemorrhaging, and other abnormalities afflictions were recorded. Individuals were scanned for a PIT-tag to document recaptures from prior juvenile sampling efforts and hatchery program releases. If no tag was detected, a PIT-tag was inserted into the ventral abdominal musculature anterior to the pelvic girdle when the individual was larger than 60 mm SL and lake conditions did not compromise sucker health (Burdick, 2011). Suckers were released at their site of capture.

Aging Juvenile Suckers

To estimate sucker age, fin rays were mounted in epoxy, sectioned, and viewed by two experienced readers using transmitted light under magnification (Quist and others, 2012). The number of annuli was determined in blind reads by two readers, with each reader having no knowledge of the other’s annuli count. When both readers agreed on a number of annuli, that number was presumed to be the correct age and was used in analyses. If there was disagreement in the annuli count, the two readers viewed the structure together and came to a consensus or a third reader acted as a tie breaker. Suckers from both lakes were either aged or assumed to be age-0 when 60 mm SL or less.

Species Identification

To identify juvenile suckers to species, we applied genetic identification methods described by Smith and others (2020 and 2023). Caudal fin tissue was collected from juvenile suckers from each lake, dried, and analyzed at the USFWS Abernathy Fish Health Center in Abernathy, Washington. Individuals were assigned to their reporting/species group described in Smith and others (2023) using genetic stock identification (GSI) implemented in the R package rubias (Moran and Anderson, 2019). The rubias package is a Bayesian approach to the conditional GSI model which includes a leave-one-out cross validation and simulation method to enhance GSI accuracy (Anderson and others, 2008). A mean posterior probability threshold of 0.9 was selected for accepting individual assignments. Only individuals assigned to a reporting/species group above this threshold were categorized to species for subsequent analyses. Fish that could not be assigned to species based on the above criteria were considered indeterminate. The current genetic technique to separate Klamath largescale from shortnose suckers was built upon known species from the Upper Klamath Basin; however, there is still uncertainty in separating these species in the Lost River Basin (Smith and others, 2020). There is a possibility that the selected markers do not translate into proper assignment of species in the Lost River Basin. A few shortnose suckers were genetically identified in the Lost River system, but most were not separated from Klamath largescale suckers and therefore were classified as the combination of Klamath largescale suckers and shortnose suckers from the Lost River Basin. Previous genetic techniques could only separate Lost River suckers from a mix of shortnose and Klamath largescale suckers (Hoy and Ostberg, 2015). In order to compare genetics across years, a category of combined shortnose and Klamath largescale suckers was included.

Indices of Juvenile Sucker Year-Class Strength and Apparent Survival

To describe annual relative (among cohorts, species, and lakes) year-class strength and age-0 sucker production, we calculated (1) the proportion of August nets to catch one or more age-0 sucker (successful age-0 nets), (2) the mean August catch per unit effort (CPUE) for age-0 suckers in successful age-0 nets, and (3) the total August age-0 CPUE as the number of suckers in each taxa divided by the number of nets set. August catches were used because this time frame represented the peak of age-0 sucker catches. We assessed age-0 summer apparent survival by comparing CPUE by year-class between the August and September sampling periods. To provide an index to compare between years, September age-0 CPUE was divided by August age-0 CPUE. If the September CPUE was greater than the August CPUE, >1 was reported indicating that suckers were recruiting to the gear at a greater rate in September than in August. We also calculated an index of fall through spring apparent survival for each year-class as the ratio of age-1 CPUE in June divided by age-0 CPUE from September from the previous year. If age-0 CPUE was zero and age-1 CPUE was greater than zero, then results were reported as >1.

We assumed that sampling efficiency was similar between years and within year sampling periods. The presence of vegetation, substrate type, and water depth have minor effects on detection probability of juvenile suckers (Burdick and others, 2008). By using the same fixed sites throughout relatively homogenous habitat with little to no vegetation, habitat variables were assumed similar at sampled sites between years. Furthermore, due to water management in Upper Klamath Lake water depth is similar each August, minimizing any effects on capture probability.

Observations on External Afflictions

We summarized the prevalence and intensity of external afflictions on juvenile suckers to compare the health of suckers between years and lakes and to identify causes of sucker mortality. We notated afflictions that are either common or potentially associated with mortality such as Lernaea sp., petechial hemorrhaging, and lamprey wounds (Markle and others, 2014; Burdick and others, 2015a). Afflictions were quantified and compared to affliction counts from previous years.

Gear Selectivity

A gear comparison study was enacted to understand if gear type selectivity was affecting catch of juvenile suckers in Upper Klamath Lake. Hoop nets (0.91-m diameter round opening, with five wire hoops for structural support, two internal round traps nets, a 9.1-m lead and two 4.6-m wing nets), large trap nets (1.2 × 16-m lead, a 1.2 × 1.8 × 1-m rectangular frame, and four 1-m diameter circular hoops [1 m apart]), and standard trap nets, as described above, were fished concurrently at five sites during June, July, and August of 2016 and five sites during July, August, and September of 2017. Sites included Fish Banks North, Fish Banks South, Mid-North, Moore Park (2016 only), Rattlesnake Point, and Shoalwater Bay (2017 only). Nets were set and fish processed using the same methods as the standard juvenile monitoring protocol. Because data did not meet the assumption of normality, the nonparametric Kruskal-Wallis test with Dunn’s multiple comparison tests were used to compare size of suckers captured and catch rates among sampling gears. A correction factor for comparing gear types was calculated by dividing the mean CPUE of large trap nets by the mean CPUE of the other gears. Burdick and Martin (2017) had indicated that their analysis could have been more complete if such a correction factor existed.

A gear comparison study was enacted to understand how standard trap nets affect sucker catches in Clear Lake. A seine (6 m long, 1.3 m high with 5 mm mesh), trammel nets (91.4 m long, 1.8 m deep; with two outer panels [30 centimeter (cm) bar], one inner panel [3.8 cm bar], a foam core float line and a lead core bottom line), and standard trap nets were used to sample suckers from June—September 2016 and 2017. Trammel nets were set for 2–3 hours during daylight hours whereas standard trap nets were fished overnight as with standard juvenile monitoring. The seine was positioned 8–15 m from dry land and parallel to shore, and then pulled directly toward shore until it was beached and fish could be removed. Fish were processed using the same methods as the standard juvenile monitoring protocol. Because data did not meet the assumption of normality, the nonparametric Kruskal-Wallis test with Dunn’s multiple comparison tests were used to compare size of suckers captured and catch rates among sampling gears.

Upper Klamath Lake Year-Class Strength and Apparent Survival

During the 2021 juvenile monitoring sampling, 85 suckers from 3 cohorts were captured in Upper Klamath Lake. Ninety-two percent were age-0 (table 3; fig. 3), 6 percent were age-1, and 2 percent were age-2. Of the 78 age-0 suckers, 35 were Lost River sucker, 41 were shortnose sucker, and 2 were Klamath largescale suckers (table 3). Age-0 suckers ranged from 36 mm to 92 mm SL (fig. 4). A total of five age-1 suckers from the 2020 cohort and two age-2 suckers from the 2019 cohort were captured throughout the sampling season in 2021 (fig. 3). Of the five age-1 suckers captured in Upper Klamath Lake, one was a Lost River sucker, one was a shortnose sucker, and three were Klamath largescale sucker. There was one age-2 shortnose sucker and one age-2 Klamath Largescale sucker that were captured in 2021. The age-1 suckers were less than or equal to 165 mm SL, whereas the age-2 suckers were 144 and 171 mm SL (fig. 5). During 2021, no captured suckers originated from USFWS SARP.

During the 2022 juvenile monitoring sampling, 19 suckers from 3 cohorts were captured in Upper Klamath Lake. Sixty-eight percent were age-0 (table 3; fig. 3), 21 percent were age-1, and 11 percent were age-2. Of the 13 age-0 suckers, 9 were Lost River sucker, 3 were shortnose sucker, and 1 was a Klamath largescale sucker (table 3). Age-0 suckers ranged from 55 to 80 mm SL (fig. 4). A total of four age-1 suckers from the 2021 cohort and two age-2 suckers from the 2020 cohort were captured throughout the sampling season in 2022 (fig. 3). Of the four age-1 suckers captured during 2022 in Upper Klamath Lake, none were Lost River suckers, three were shortnose suckers, and one was a Klamath largescale sucker (table 3). There was one age-2 shortnose sucker and one age-2 Klamath Largescale sucker that were captured in 2022. The age-1 suckers were ≤130 mm SL, whereas the age-2 suckers were 143 and 190 mm SL (fig. 5). During 2022, no captured suckers originated from USFWS SARP.

August CPUE of age-0 suckers for all sucker species combined in Upper Klamath Lake was low in 2021 and 2022. The 2022 August CPUE was the lowest on record whereas the 2021’s August CPUE was similar to those recorded in 2018. There was an even mix of Lost River and shortnose suckers captured in August of 2021, whereas most of the age-0 suckers captured during August of 2022 were Lost River suckers (table 4). Age-0 Lost River Sucker CPUE in 2021 was similar to 2018 and 2020, but larger than in 2017 and 2022, and only about 10 percent of CPUE in 2016 (table 4). Age-0 Lost River Sucker CPUE in 2022 was similar to 2017, with both representing the lowest on record (table 4). The 2021 shortnose sucker CPUE was similar to that in 2017 and was lower than in most other sampling years except for 2018, 2020, and 2022. The 2022 shortnose sucker CPUE was similar to 2018 and 2020, with all three being the lowest on record (table 4).

The CPUE from the 2019 and 2020 cohort declined through 2021 and 2022 sampling. CPUE of the 2019 cohort decreased to near zero starting in July 2020 and were last captured in June 2021 (table 5). CPUE of the 2020 cohort started to decline in August of 2020 and was also last detected in September of 2022 (table 6). CPUE of the 2021 cohort started to decline in August of 2021 and was last detected in July of 2022 (table 7). Contrary to other years, the 2021 cohort appeared to be fully recruited to the gear already in July (table 7), whereas the 2022 cohort did not recruit to the gear until August (table 8). Age-0 catch rates for the 2021 cohort declined between July and August and again between August and September (table 7), whereas age-0 catch rates for the 2022 cohort declined between August and September (table 8).

Apparent survival of all suckers from August to September varied by year with the overall highest apparent survival occurring in 2018, 2020, 2021, and 2022 (table 9). However, survival indices in these years were driven by the high apparent survival of the combination of shortnose and Klamath largescale suckers, which had larger catches in September than in August. This indicates that these suckers were likely recruiting to the nets in September (table 9). Shortnose suckers/Klamath largescale suckers had greater apparent survival from August to September than Lost River suckers within most years (table 9). The 2017 and 2019 cohorts were the only ones that had greater August to September apparent survival for Lost River suckers, with survival indices high in 2019 and low in 2017 (table 9). The remaining Lost River cohorts had low apparent survival with indices ≤0.20. The August to September apparent survival for the 2015, 2016, and 2019 cohorts of shortnose/Klamath largescale suckers was moderate (indices ranged from 0.35 to 0.49), whereas it was zero for the 2017 cohort. When considering only genetically identified shortnose suckers, August to September survival indices were 0.19 in 2021 and greater than 1.00 in 2020 and 2022. This indicates that the 2021 cohort of shortnose suckers had poor survival from August to September 2021.

Fall through spring apparent survival varied by taxa and cohort. The 2017 shortnose/Klamath largescale sucker cohort had the highest fall through spring survival index. Shortnose/Klamath largescale suckers had greater fall through spring survival than Lost River suckers within most years (table 10), the exception being the 2015 cohort of Lost River suckers. The 2015 Lost River sucker cohort had the highest fall through spring survival index (0.75), whereas the 2020 cohort had a moderate index (0.33), compared to the indices (0–0.06) for the remainder of Lost River sucker cohorts (table 10). Shortnose/Klamath largescale suckers had the highest fall through spring survival indices for the 2017 and 2019 cohorts (>1 and 0.92), with moderate fall through spring survival indices for the 2015 and 2020 cohorts (0.33 and 0.44; respectively), and poor fall through spring survival indices for 2016, 2018, and 2021 cohorts (table 10). The 2021 cohort of genetically identified shortnose suckers had poor fall through spring survival index of 0.00 from September to June. Although the 2021 cohort was not detected in June of 2022, it was detected after June 2022.

Clear Lake Reservoir Year-Class Strength and Apparent Survival

The majority of suckers captured in Clear Lake Reservoir in 2021 and 2022 were classified as Klamath largescale suckers and shortnose suckers from the Lost River Basin. These fish were 3–5 years old and ranged from 142 to 335 mm SL (figs. 3, 5). In 2021, there were two age-2 suckers and three age-6, and one recaptured sucker that was assumed to be age-7. In 2022, there was one age-2 sucker captured. One age-2 sucker, classified as a Klamath largescale sucker and shortnose sucker from the Lost River Basin was tagged in June 2021 (153 mm SL) and recaptured in September 2021 (175 mm SL). None of the 106 unique suckers captured in Clear Lake Reservoir during the 2021 or the 79 suckers captured in 2022 juvenile monitoring sampling were age-0 or age-1 (fig. 3; table 11). Only 3 of the 106 suckers captured in 2021 were classified as Lost River suckers; 1 was classified as a shortnose sucker and 3 did not have genetic samples taken (figs. 3, 5). Two of the suckers that did not have genetic samples taken were morphologically identified as Klamath largescale suckers and were known recaptures from previous years (285 and 399 mm SL). Only 2 of the 79 suckers captured in 2022 were classified as shortnose suckers; none was classified as Lost River sucker; and 2 did not have genetic samples taken (figs. 3, 5). All suckers classified as Lost River or shortnose suckers were from the 2016 and 2017 cohorts.

The age distribution of suckers in Clear Lake indicates that juvenile suckers are surviving beyond the juvenile life stage. In 2021, the largest sucker captured in Clear Lake was 399 mm SL. It was not aged because it was a recaptured sucker that had originally been captured and tagged in a different study. The largest sucker captured in 2022 was 402 mm SL and was not aged (fig. 3). The oldest sucker captured in 2021 appeared to be an age-7 sucker. It was initially captured in 2020 and was identified as age-6 at that time. The oldest aged sucker captured in 2022 was age-5 and 306 mm SL. In 2021, we captured five age-6 suckers from the 2015 cohort. The most abundant cohorts captured in 2021 were from 2016 (age-5), 2017 (age-4) and 2018 (age-3), whereas the most abundant cohorts captured in 2022 were from 2017 (age-5), 2018 (age-4), and 2019 (age-3). In 2021, two age-2 suckers from the 2019 cohort were captured (one captured twice). In 2022, only one age-2 sucker from the 2020 cohort was represented in our catches. No age-0 or age-1 suckers were captured in Clear Lake in 2021 or 2022.

There were several year-classes of suckers that were not captured as age-0 suckers; however, these year-classes were captured for the first time starting at as early as age-1 (table 12). The peak of the 2015 cohort catches was during the September 2017 sampling effort, or when the cohort was age-2 (table 12). Very few fish from the 2015 cohort were captured in 2021 and by 2022 these fish may have been too large to recruit into our trap nets. The 2016 cohort catches peaked during September 2016 when the cohort was age-0 and were no longer detected in our sampling gear in 2022. The 2017 cohort catch peaked during the June 2019 sampling effort when the cohort was age-2. The 2018, 2019, and 2020 cohort catches all peaked during June 2022 sampling effort when the cohorts were age-4, age-3, and age-2, respectively. However, catch rates for the 2018 and 2019 cohorts were consistently low throughout the years other than 2022. Only the 2016 and 2017 cohorts were detected for the first time at age-0. The 2015, 2018, and 2019 cohorts were first detected at age-1. The 2020 cohort was first detected in 2022 with one age-2 fish detected. The 2021 and 2022 cohorts have not yet been detected and if detected in 2023 would be detected at age-2 and age-1 respectively.

Afflictions

Suckers in Upper Klamath Lake often had more macro parasites, deformities, and skin afflictions than suckers in Clear Lake. The primary affliction observed during the 2021 and 2022 monitoring seasons in both lakes was Lernaea sp. Other afflictions observed were lamprey wounds on eight Clear Lake suckers in 2021 and four suckers in 2022, and petechial hemorrhages on one Upper Klamath Lake sucker in 2021. In 2021 and 2022, we did not observe any fish with black spot (metacercariae of Bolbophorus spp.) from either lake (table 13).

Missing or deformed opercula were only observed on one Upper Klamath Lake sucker in 2021 (table 14). It was an age-0 shortnose sucker that had both opercula missing or deformed. Opercular deformities tend to be more common in Lost River suckers than shortnose suckers. Opercular deformities occurred in Lost River suckers from 0 to 62 percent of the time within each year, whereas this deformity occurred less than 10 percent of the time in shortnose suckers within each year.

All Lernaea sp. observations in age-0 suckers occurred from Upper Klamath Lake (table 15). In both 2021 and 2022, age-1 and older suckers in Upper Klamath Lake had a lower proportion of fish with Lernaea sp. attached than those in Clear Lake (table 16). In 2021, there were more Lernaea sp. reported per individual sucker in both lakes with the most attached to an individual juvenile sucker reported as 21 from an age-0 Lost River sucker in Upper Klamath Lake. Although this parasite was a relatively common occurrence in both Upper Klamath Lake and Clear Lake, there were no obvious signs that Lernaea sp. causes direct mortality of juvenile suckers.

Petechial hemorrhaging of the skin on age-0 fish was only observed in one Upper Klamath Lake sucker in 2021 (table 17). The proportion of age-0 suckers in Upper Klamath Lake with petechial hemorrhaging in 2021 was low relative to previous years, and nonexistent in 2022 (table 17). In 2021 and 2022, petechial hemorrhaging was not observed on age-1 and older suckers in both lakes (table 18).

Gear Selectivity

The majority of suckers captured in all three gear types (large trap nets, standard trap nets and hoop nets) used in Upper Klamath Lake were age-0 suckers during both years (fig. 6; table 19). In 2016, SL did not vary among gear types (Kruskal-Wallis, p=0.456). In 2017, SL varied by gear type (Kruskal-Wallis, p<0.001) likely because the standard trap nets captured few but larger individuals, 4 of which were greater than 100 mm SL. Age-0 and age-1 juvenile suckers were captured in all three gear types.

Catch rates in Upper Klamath Lake varied greatly among gear types (Kruskal-Wallis, p<0.001; table 19). Dunn multiple comparison tests indicated that large trap nets had the highest catch rates (p<0.001), whereas hoop nets and standard trap nets had similar catch rates (p=0.568). Given that standard trap nets captured few fish in 2017, the 2016 catch rates were used to calculate the correction factor for comparison of hoop nets and standard trap nets to large trap nets. The resulting correction factors were 4.8 for hoop nets and 5.4 for standard trap nets.

Each gear type (standard trap net, trammel net, and seine) in Clear Lake captured different size classes of sucker (Kruskal-Wallis, p<0.001; fig. 7; table 20). Dunn multiple comparison tests indicated that all gear types captured different sizes (all p<0.001). Trammel nets primarily captured adults, seines captured small juveniles, and standard trap nets captured juveniles greater than 54 mm and few adults. The difference in sizes between seines and standard trap nets indicates that standard trap nets are biased for larger juveniles (>54 mm SL).

Upper Klamath Lake

The lack of substantial recruitment to the spawning population continues to be the bottleneck for the recovery of shortnose and Lost River suckers in Upper Klamath Lake. Since the early 2000s, the abundance of both species has decreased by more than 40 percent (Hewitt and others, 2018). Nearly all adult suckers in Upper Klamath Lake are older than the average life span expected for each species, and shortnose suckers are approaching the maximum known age for their species (Hewitt and others, 2018; Krause and others, 2022). As the adult sucker populations diminish, we continue to catch small numbers of juvenile suckers during our monitoring efforts. Without the balance of recruitment by new individuals to the spawning population, Lost River and shortnose suckers will continue their downward population trend in Upper Klamath Lake.

The scarcity of age-1 and older suckers in Upper Klamath Lake is likely attributable to juvenile mortality. Several observations support the presumption that mortality, rather than reduced gear selectivity or emigration from sampled areas, explains the reduction in catch by age. Most of our catch in Clear Lake were age-2 and older suckers, indicating older, larger fish are vulnerable to our trap nets and therefore gear selectivity does not contribute to the lack of age-1 and older suckers in Upper Klamath Lake. A substantial lack of recruitment to the adult populations in Upper Klamath Lake indicates that juvenile suckers have unsustainably low survival rates (Hewitt and others, 2018). A lack of directed movement toward the lake’s outlet suggests that emigration is not the primary reason for a lack of older juvenile suckers in Upper Klamath Lake (Burdick and others, 2009b).

Although mortality is substantial for Lost River and shortnose suckers, it appears to be greater for juvenile Lost River than shortnose suckers as seen by the fall through spring survival indices. Although earlier years did not separate out shortnose suckers from Klamath largescale suckers, there was a separation between these two species starting in 2020. Age-1 catch was composed of a greater number of shortnose suckers than Lost River or Klamath largescale suckers in 2020 and 2022, whereas Klamath largescale suckers composed a greater portion of the age-1 catch in 2021. There is always the possibility that the index for past years reflects a greater portion of Klamath largescale suckers surviving to age-1; however, the lack of age-1 Klamath largescale suckers captured during 2020 and the low number captured in 2022 and the identification of more shortnose suckers than Klamath largescale suckers using vertebrae counts in past studies (Burdick and others, 2008, 2009a; Burdick and Brown, 2010) suggest that the past 7 years may also have a minimal proportion of age-1 Klamath largescale suckers. Burdick and Martin (2017) reported the same survival trend; however, they were unable to determine why there were differences in species mortality rates. We hypothesize that Lost River suckers, which hatch earlier than shortnose suckers, may encounter unfavorable environmental conditions (for example, water quality or food availability) at a critical juncture in their development.

There are several possible explanations for why we only detected one of the thousands of PIT-tagged suckers that were released into Upper Klamath Lake from the SARP program through 2022. Given the large size of Upper Klamath Lake, these are relatively small numbers of fish to detect, even when ignoring post-release mortality. PIT-tag antennas operating in the Link River at the outlet of Upper Klamath Lake and in the Williamson and Sprague Rivers have detected less than 1 percent of the SARP fish released from 2018 through 2022 (151 out of 41,800 as of December 31, 2022), indicating that directed emigration was an unlikely explanation for the disappearance of these fish (Krause and others, 2023). Furthermore, the majority of the 151 detected fish (76 percent) were detected in 2021, whereas 21 percent were detected in 2022. As of the writing of this report, USGS crews have detected 248 (<1 percent) of the PIT tags from SARP-released suckers on bird colonies cumulatively from 2018 through 2022 scanning efforts, indicating bird predation may be a factor in the survival of some SARP fish (Evans and others, 2016). However, Evans and others (2022) estimated that predation rates on SARP fish ranged from 4.3 (95 percent credible interval = 2.9–6.7 percent) to 8.5 percent (6.3–12.7 percent) percent annually from 2018 through 2020, indicating that colonial bird predation accounts for a small percentage of the mortality of these suckers.

Although it is typical for survival to be low in the early life stages of fish (Houde, 1989), near-complete disappearance of entire cohorts within the first 2 years is of concern. High fecundity may be a life-history strategy to overcome high mortality for juvenile suckers in the Klamath Basin, but near complete mortality is unsustainable (Rasmussen and Childress, 2018). Although age-0 apparent survival was intermediate from August–September for the 2019 cohort compared to age-0 apparent survival of other cohorts, the fall through spring apparent survival of the 2019 cohort was low, resulting in a substantial loss of this cohort. Given that the adult populations of Lost River and shortnose suckers have decreased by more than 50 percent since the early 2000s (Hewitt and others, 2018), there would have to be a substantial recruitment event in the coming years for both species to recover. As of the writing of this report, we have no indication that such an event is imminent.

Clear Lake Reservoir

With greater juvenile sucker survival than in Upper Klamath Lake, intermittent recruitment of new spawners has been documented for Clear Lake populations (Hewitt and Hayes, 2013). The mechanisms behind intermittent cohort success are not completely understood. Hypotheses include (1) limited access to spawning habitat in dry years and (2) differential juvenile sucker mortality among years. It has been shown that varying rates of juvenile sucker mortality are associated with differential rates of avian predation among years that are mediated by water levels and fish size, especially for small fish (Evans and others, 2022). Another hypothesis of why survival is better in Clear Lake than Upper Klamath Lake include the differences in water quality between the two lakes, and that the Clear Lake population is believed to be composed mainly of Klamath largescale suckers, which can rear in the river before entering the lake.

A lack of age-0 suckers captured in the low water years of 2014 and 2015 in Clear Lake Reservoir led Burdick and others (2016) to conclude cohorts were not formed in those years. Lake-surface elevations less than 1,378.9 m prevented adult suckers from migrating up the spawning tributaries in the spring of both years (Hewitt and others, 2021), and during the current sampling year of 2022 (fig. 8). Burdick and others (2016) had concluded that spawning did not occur without access from the lake to the river. After high flows in the Willow Creek drainage increased lake-surface elevations in 2016 (fig. 8), the 2014 and 2015 cohorts were detected in Clear Lake Reservoir. The 2014 cohort was collected through 2020 and the 2015 cohort was collected through 2021. Lack of collection of these cohorts after these time frames was most likely due to the suckers being too large to recruit to the standard trap nets used during our surveys. The presence of the 2015 juvenile cohort in Clear Lake challenged the Burdick and others’ (2016) presumption that high springtime lake elevations are required to form year-classes in Clear Lake Reservoir (Bart and others, 2020a). We suspect that the majority of the 2015 cohort are offspring of stream resident Klamath largescale suckers that only recruited to Clear Lake when high water flushed them from the tributaries. Although the current genetic techniques can separate Klamath largescale suckers from shortnose suckers in the Klamath Basin, there is still uncertainty in separating these species in the Lost River Basin (Smith and others, 2020). Suckers from the 2015 cohort were genetically classified as the combination of Klamath largescale suckers and shortnose suckers from the Lost River Basin. However, a stream resident life history is consistent with these fish being Klamath largescale suckers.

The lack of access between the tributaries and Clear Lake does not explain why age-0 sucker catches were absent in 2018–21. Lake levels were relatively high, and adult suckers were detected on remote PIT-tag arrays migrating into Willow Creek during springs of 2018–19, indicating that spawning likely occurred (Hewitt and others, 2021). With higher water levels and access to Willow Creek for spawning habitat, we expected to see large numbers of age-0 suckers in Clear Lake from 2018 to 2021, but this was not the case. Creek flows were relatively low in all years except for 2016, 2017, and 2019 (fig. 8). Furthermore, the duration of high flows in 2016, 2017, and 2019 appeared long enough to support spawning (fig. 8). The high water discharge years coincide with the observance of age-0 suckers in 2016 and 2017, but not 2019. It would appear that 2019 should have had proper conditions for age-0 suckers to be present; however, there was a huge fire in 2019 that burned along the shoreline (https://en.wikipedia.org/wiki/Tucker_Fire, and personal observation) and may have negatively impacted this year class in the lake. In the remaining years, a lack of sufficient spring discharge could have prevented age-0 suckers from outmigration to the lake thus trapping suckers in disconnected pools. Juvenile and adult suckers have been documented in disconnected pools and reservoirs throughout the Willow and Boles Creek drainages during summer 2018 (Martin and others, 2021).

Genetic analysis of the sucker species in Clear Lake indicate that there are very few Lost River or definitive shortnose suckers. The only cohorts represented by Lost River and shortnose suckers are the 2016 and 2017 cohorts. To date, the genetically identified group of Klamath Largescale and shortnose suckers from the Lost River Basin represent all cohorts tracked through this study except for the 2021 and 2022 cohorts. Given our continued pattern of catching cohorts once they are past age-0 or age-1, sampling Clear Lake in 2023 is needed to confirm the possible existence of the 2021 and 2022 cohorts. This information combined with the above cohort tracking indicates that the category of Klamath Largescale and shortnose suckers from the Lost River Basin most likely represents Klamath Largescale suckers.

Clear Lake surface elevation and Willow Creek flows may affect the annual rate of bird predation on suckers (Hewitt and others, 2021). Double-crested cormorants (Nannopterum auritum) and American white pelicans (Pelecanus erythrorhynchos) prey upon vulnerable suckers as they enter Willow Creek to spawn. Hewitt and others (2021) hypothesized that adult sucker mortality is greatest when lake-surface elevation ranges from 1,378.9 to 1,379.2 m above mean sea level during the spawning migration. Several cohorts that cease to be captured in trammel net catches at the age of first spawning may indicate that young or small adult suckers are especially vulnerable to bird predation. When the lake-surface elevation is less than 1,378.9 m or if instream flows are very low, suckers cannot access spawning habitat in Willow Creek and are therefore less susceptible to predation. The formation of nesting islands for American white pelican and double-crested cormorant at lake-surface elevations greater than 1,378.9 m provides protection for the birds’ eggs from predators, resulting in greater numbers of birds to be present for a longer period (Evans and others, 2016). As lake-surface elevation increases above 1,378.9 m, bird islands shrink in size, thus reducing bird nesting habitat and the number of nesting birds available to prey on suckers. At lake-surface elevation above 1,379.2 m, deep water also provides cover for migrating suckers (National Marine Fisheries Service and U.S. Fish and Wildlife Service, 2013). Poor survival of suckers that first attempt to spawn in low-water years may explain the absence of some cohorts from adult sucker sampling.

Afflictions

Opercular deformities, which are more common for Lost River than shortnose suckers, make the gills more vulnerable to parasites and poor water quality and ultimately increase the chance of mortality. Because there were no age-1 or older suckers in Upper Klamath Lake with deformed opercula, there is the potential that it is serious enough of an affliction that it increases the probability of mortality before fish can reach older ages. However, we did see opercular deformities in several of the age-4 suckers classified as the combination of Klamath largescale suckers and shortnose suckers from the Lost River Basin in Clear Lake in 2020, indicating there may be additional confounding factors. Although this affliction has been observed on other sucker species (Barkstedt and others, 2018), the exact cause of deformed opercula is difficult to determine. Potential explanations could be inbreeding, hybridization (Winemiller and Taylor, 1982; Tringali and others, 2001), nutrient deficiency (Chávez de Martínez, 1990; Lall, 2002), heavy metals, pesticides, high egg incubation temperature (Boglione and others, 2013) or a combination of these factors.

Lernaea sp. parasitism is one of the most common afflictions on juvenile suckers captured in both lakes, occurring to some degree in all sampling years. Wounds that form at Lernaea sp. attachment sites may provide a pathway for bacterial infection (Berry and others, 1991). Inflammation associated with Lernaea sp. attached to juvenile suckers from Upper Klamath Lake is most often limited to a focal area in the skin and skeletal muscle directly surrounding the attachment site, indicating this parasite is unlikely to cause systemic infections that result in mortality (Burdick and others, 2015a). However, when an individual sucker is highly parasitized with Lernaea sp. as seen during 2021, when 1 individual supported 21 of these parasites, the likelihood of adverse effects increases. Several studies indicate that infestation of Lernaea increase with increased temperatures, with ideal transmission occurring from 23 to 30 °C (Marcogliese, 1991; Sánchez-Hernández, 2017).

The causes of petechial hemorrhaging, which generally appears more frequently on suckers from Upper Klamath Lake, are unknown. Petechial hemorrhages of the skin are a common observation in Upper Klamath Lake and have been documented since affliction monitoring began in 2014 (Burdick and others, 2015a). Petechial hemorrhages of the skin have been found to be caused by irritants including abrasion, bacteria, or toxins (Ferguson and others, 2011). The low prevalence of observed hemorrhages in Clear Lake relative to Upper Klamath Lake indicates that abrasions caused by our method of capture is unlikely to be the primary reason for the hemorrhaging. Burdick and others (2018) examined the hemorrhages microscopically and did not observe associated bacterial disease or other parasites. Janik and others (2018) observed petechial hemorrhaging on collected fish from Upper Klamath Lake canals; however, they could not observe it through histology, which indicated that the infection was likely confined to the skin.

Lamprey wounds were seen in both lakes but are likely not a large source of mortality. All lamprey species in the Upper Klamath Basin are native (Kostow, 2002). Given the low prevalence of lamprey wounds and that lamprey have coevolved with suckers in the Klamath Basin, it is unlikely that they are the primary cause of annual juvenile sucker year-class failure.

Incidence of black spot was hypothesized to be associated with high mortality of juvenile suckers (Markle and others, 2014). In previous years monitoring, black spot was only recorded on a small proportion of fish, and during the 2018–22 monitoring seasons, there were no suckers with black spot (Bart and others 2020a, b; Bart and others, 2021; Martin and others, 2022). In years when black spot was observed, it was more prevalent in Upper Klamath Lake than in Clear Lake (Burdick and others, 2016, 2018; Bart and others, 2020b). There is the potential that we are missing cases of black spot in suckers when it is not externally visible. Markle and others (2020) found that out of 55 fish observed without external black spot, 10 had internal muscle or gill infections of black spot. Although this would indicate that black spot is underrepresented in our data, there is no indication from our data that it is a substantial source of mortality for juvenile suckers.

Gear Selectivity

Various gears have been used to capture suckers in Upper Klamath and Clear Lakes since USGS began sampling for juvenile suckers in 2001. In Upper Klamath Lake, the primary gears used to collect juvenile suckers from 2001 through 2006 were large trap nets and hoop nets. Starting in 2007, the primary gear used was standard trap nets (Burdick and Martin, 2017). Burdick and Martin (2017) stated that in order to compare the gear types from different years a comparison factor needed to be determined based on the different gear types being fished simultaneously. After finding that catch rates differed among gear types, which prevented direct comparisons, we calculated a correction factor based on the 2016 sampling. However, given that only 1 year of data was used in the calculation, the resulting adjusted CPUEs should be considered approximate and comparisons to actual CPUEs should be made cautiously.

When comparing gear types, the inferences on the size selectivity differed by lake system. Gear types in Upper Klamath Lake did not appear to have a size bias given that all gears caught age-0 suckers. However, because minimal numbers of age-1+ juveniles were captured in Upper Klamath Lake, it is unclear how the size selectivity differs between gears for older juveniles. In previous Clear Lake studies, trammel nets had been used to collect subadult and adult suckers, whereas standard trap nets and seines had been used to collect juvenile suckers (Burdick and Rasmussen, 2012; Hewitt and others, 2021; Martin and others, 2022). Comparison of these gear types corroborated our suspicions that seines selected for the smaller juvenile suckers, standard trap nets selected for larger juvenile suckers and subadult suckers, whereas trammel nets selected for the subadult and adult suckers. Age-0 suckers were collected in both the seines and standard trap nets indicating that both sampling techniques are able to detect age-0 suckers if they are present in Clear Lake in any given year. However, seining proved to be a difficult and somewhat ineffective method of capturing suckers because of the presence of large boulders or deep muck.