The largest populations of federally endangered Lost River (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) exist in Upper Klamath Lake, Oregon, and Clear Lake Reservoir, California. Upper Klamath Lake populations are decreasing because adult mortality, which is relatively low, is not being balanced by recruitment of young adult suckers into known spawning aggregations. Most Upper Klamath Lake juvenile sucker mortality appears to occur within the first year of life. Annual production of juvenile suckers in Clear Lake Reservoir appears to be highly variable and may not occur at all in very dry years. However, juvenile sucker survival is much higher in Clear Lake, with non-trivial numbers of suckers surviving to join spawning aggregations. Long-term monitoring of juvenile sucker populations is needed to (1) determine if there are annual and species-specific differences in production, survival, and growth, (2) to identify the season (summer or winter) in which most mortality occurs, and (3) to help identify potential causes of high juvenile sucker mortality, particularly in Upper Klamath Lake.

We initiated an annual juvenile sucker monitoring program in 2015 to track cohorts in 3 months (June, August, and September) annually in Upper Klamath Lake and Clear Lake Reservoir. We tracked annual variability in age-0 sucker apparent production, juvenile sucker apparent survival, and apparent growth. Using genetic markers, we were able to classify suckers as one of three taxa: shortnose or Klamath largescale suckers, Lost River, or suckers with genetic markers of both species (Intermediate Prob[LRS]). Using catch data, we generated taxa-specific indices of year class strength, August–September apparent survival, and overwinter apparent survival. We also examined prevalence and severity of afflictions such as parasites, wounds, and deformities.

Indices of year class strength in Upper Klamath Lake were similar for shortnose suckers in 2015 and 2016, but about twice as high for Lost River suckers and suckers having intermediate Prob[LRS] in 2016 than in 2015. Indices of apparent August–September survival were lower in 2016 (0.41) than in 2015 (1.07) for shortnose suckers and suckers identified as having intermediate Prob [LRS] (0.14 in 2016 and 1.69 in 2015). Indices of apparent August—September survival were similar in 2016 (0.16) and 2015 (0.07) for Lost River suckers. Indices of apparent survival were lower for age-0 Lost River suckers than age-0 shortnose suckers in both years. Although samples sizes are small, a declining trend in the ratio of Lost River to shortnose suckers from 28/23 (1.22) as age-0 fish in September of 2015 to 1/9 (0.11) as age-1 fish in June of 2016 is consistent with higher over winter apparent mortality for Lost River suckers than shortnose suckers in Upper Klamath Lake.

Shortnose sucker year class strength was greater in years with high Willow Creek inflows and Clear Lake surface elevation during the spawning season, indicating that access to spawning habitat was an important contributing factor. In previous sampling, age-0 sucker catch per unit effort (CPUE) was relatively high in 2011 and 2012, moderately high in 2013, and zero in 2014 and 2015. The 2011 and 2012 year classes continued to be detected, but the 2013 year class went undetected for the first time in 2016. The 2014 year class continued to be undetected in 2016. Three suckers with one annulus each on fin rays were captured in Clear Lake in 2016. Although these fish are potential representatives of the 2015 year class, they were small for their age, indicating they may have hatched in 2016. Age-0 shortnose and Lost River suckers were captured in Clear Lake in 2016, indicating new cohorts of both taxa were produced. Moderate to abundant year classes were produced in 2011, 2012, and 2016 when lake surface elevation greater than 1,378.9 m (4,524 ft) during the February–June spawning season. Also in 2011 and 2016, rapid increases in lake-surface elevation indicated potentially high Willow Creek inflows. A somewhat less abundant year class produced in 2012 than in 2011 and 2016 was associated with lower spawning season inflows. The apparently smaller 2013 year class was formed when Willow Creek inflows were apparently low and lake surface never exceeded 1,379.2 m (4,524.9 ft). In 2014 and 2015, when year-classes were small or not detected, the Clear Lake surface elevations were at or below 1,378.2 m (4,522 ft), and there was very little spring time Willow Creek inflow.

Age-0 shortnose sucker CPUE in Clear Lake was correlated with seasonal decreases in water volumes in 2016 and could not be used to create indices of August–September survival. Age-0 shortnose sucker catch rates in Clear Lake Reservoir were about seven times less in August than in September. Meanwhile, the water volume in Clear Lake Reservoir declined by about 36 percent between these two sampling periods. Higher September catch rates may have resulted from additional age-0 suckers entering the lake from the river, a concentrating effect of declining water volumes, or both.

Differences in August standard length, apparent growth rates, and the prevalence of abnormalities were consistent with healthier age-0 suckers in Clear Lake Reservoir than in Upper Klamath Lake. Age-0 suckers were larger in August in Clear Lake Reservoir than in Upper Klamath Lake, which may be due to an earlier hatch date, faster growth, or both in Clear Lake Reservoir. Sample sizes were only large enough to compare growth rates of age-0 shortnose suckers from Upper Klamath Lake in 2015 to Clear Lake Reservoir in 2016. Age-0 shortnose suckers grew more between August and September in Clear Lake Reservoir in 2016 than in Upper Klamath Lake in 2015. Petechial hemorrhages of the skin on age-0 suckers were more prevalent in Upper Klamath Lake than in Clear Lake Reservoir in 2016. Deformed opercula, black-spot forming parasites, and infections presumed to be Columnaris sp. were observed on less than 12 percent of suckers from Upper Klamath Lake but were not observed on suckers from Clear Lake Reservoir in 2016.