Geology topics

Research about California, Oregon

Source-linked reports with geographic coverage including California, Oregon.

At least 55 records · Page 3Linked to original sources

USGS2019

Application of the Stream Salmonid Simulator (S3) to Klamath River fall Chinook salmon (Oncorhynchus tshawytscha), California—Parameterization and calibration

Executive Summary In this report, we describe application of the Stream Salmonid Simulator (S3) to Chinook salmon ( Oncorhynchus tshawytscha ) in the Klamath River between Keno Dam in southern Oregon and the ocean in northern California. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. It can track different source populations or species, such as major tributary populations that enter a river like the Klamath River. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit affect survival and growth within each habitat unit and movement of fish among habitat units. The physical template of the Klamath River was formed by classifying the river into 2,635 mesohabitat units composed of runs, riffles, and pools. This template enabled modeling of the unimpounded Klamath River between the Keno Dam (the uppermost of four dams) and Iron Gate Dam (the lowermost dam) to address dam-removal scenarios. However, in this report, our focus was on parameterizing and calibrating the model under existing conditions, which included 1,706 discrete habitat units over the 312-kilometer (km) section of river between Iron Gate Dam and the ocean. For each habitat unit, we developed a time series of daily flow, water temperature, and amount of available habitat (weighted usable habitat area [WUA]) for spawners, fry, and parr. WUA time series were constructed using habitat suitability criteria for Chinook salmon applied to eight two-dimensional (2-D) hydrodynamic models that represented the geomorphic variability in habitat across the Klamath River. Results from the 2-D models were then extrapolated to unmodeled habitat units by scaling WUA curves for changes in habitat unit length and width. These variables were then used to drive population dynamics such as egg development and survival and juvenile movement, growth, and survival.

California, Oregon↗

USGS2019

Using the precipitation-runoff modeling system to predict seasonal water availability in the upper Klamath River basin, Oregon and California

Accurate forecasts of the streamflow expected during late spring and summer in the Upper Klamath River Basin in southern-central Oregon and northern California are used by water management agencies to balance water allocations for agriculture, aquatic habitat, and hydropower-production needs. Streamflow forecasts are also used by irrigation farmers for planning. The forecasts are typically made twice a month starting as early in the water year as December. Multiple regression equations relating real-time snowpack and precipitation conditions to seasonal streamflow volumes have been used for many years in forecasting. However, with warming temperature trends and lower snowpack, such forecasts based on historical data could become less reliable in the future. If the timing and relation of snowpack and precipitation are outside of the range of the historical data used to create the equations, the forecasts become extrapolations. Statistical forecast equations are also limited in their ability to forecast streamflow in groundwater-dominated basins having inter-annual lag. As an additional method for seasonal streamflow forecasting, a physical-process-based hydrologic model employing the Precipitation-Runoff Modeling System (PRMS) was developed in cooperation with the U.S. Bureau of Reclamation for the Upper Klamath Basin in this study. The model was calibrated for the portion of the basin draining into Upper Klamath Lake. PRMS is a deterministic, distributed-parameter, physical-process-based modeling system developed by the U.S. Geological Survey. It simulates daily streamflow, snow, solar radiation, evapotranspiration, surface-water, and groundwater processes within the basin. A model calibration and validation period for water years 2000–15 and water years 1984–99, respectively, was used. The model was calibrated and validated using measured streamflow, snowpack, evapotranspiration, and solar radiation data sets. Interpolated daily precipitation and air temperature data from 32 meteorological stations within and surrounding the Upper Klamath Basin were used as model input. Performance statistics, used to evaluate how well simulated daily streamflow matched with measured streamflow included percent bias, percent relative error, and root-mean-square error. The statistics were computed annually, monthly, for October–March, and for April–September. With the exception of the October–March period, percent bias statistics were all within plus or minus 5-percent for both the calibration and validation periods. Limitations to using the model are error in the precipitation and air temperature input time series data, which include measurement error and error in the spatial interpolation method. Other errors include measured daily streamflow data, which were adjusted for consumptive use losses to make them more closely resemble natural streamflow for calibration. The model developed for the Upper Klamath Basin can be used to forecast streamflow from the Sprague and Williamson River Basins and inflow to Upper Klamath Lake. Reliable forecasts at these locations are needed for managing water for irrigation, ecosystem health, and power production. Using the models in a forecast application requires assembling model input data sets of anticipated daily precipitation and minimum and maximum air temperature for the period after the date the forecast is made and the end of the forecasted period. These climate data sets can be based on historical or synthetic records, at the discretion of the forecaster. With the Ensemble Streamflow Prediction method, a suite of streamflow scenarios is simulated using multiple years of climate data as model input. The forecasted streamflow is determined from knowing the exceedance probabilities of the simulated streamflows. In this study, the model and the Ensemble Streamflow Prediction method were used to forecast the volume of inflow to Upper Klamath Lake for a 6-month period from April 1, 2015, to September 30, 2015, using a range of climate data sets based on El Niño Southern Oscillation (ENSO) criteria. Because 2015 was a warm phase ENSO period, climate data for 10 warm phase ENSO years from 1980 to 2010 were used as input to the model. The simulated April–September 2015 UKL inflow volume based on measured 2015 climate data was 482,000 acre-feet, which was very close to the 50th percent exceedance probability computed from 10 simulated scenarios that used warm phase ENSO climate input data from 1980–2010.

California, Oregon↗

USGS2019

Evolutionary dynamics of Ceratonova species (Cnidaria: Myxozoa) reveal different host adaptation strategies

The myxozoan parasite Ceratonova shasta is an important pathogen that infects multiple species of Pacific salmonids. Ongoing genetic surveillance has revealed stable host-parasite relationships throughout the parasite's endemic range. We applied Bayesian phylogenetics to test specific hypotheses about the evolution of these host-parasite relationships within the well-studied Klamath River watershed in Oregon and California, USA. The results provide statistical support that different genotypes of C. shasta are distinct lineages of one species, which is related to two other Ceratonova species in the same ecosystems; Ceratonova X in speckled dace and C. gasterostea in threespine stickleback. Furthermore, we found strong support for the hypothesis that C. shasta type 0 in native steelhead trout and type I in Chinook salmon each evolved with a specialist host adaptation strategy, while C. shasta type II in coho salmon resulted from a generalist host adaptation strategy. Inferred date and host species of the most recent common ancestor of extant Klamath basin types indicate that it occurred between 14,000 and 21,000 years ago, and most likely infected a native steelhead or rainbow trout host.

California, Oregon↗

USGS2019

Estimating annual Ceratonova shasta mortality rates in juvenile Scott and Shasta River coho salmon that enter the Klamath River mainstem

The impacts of Ceratonova shasta on Klamath River salmonids have been the focus of tremendous research and monitoring over the past decade. Knowledge gained from the various studies has resulted in a growing suite of decision support tools that can be used to predict the prevalence of infection and mortality that can be expected from varying exposure concentrations to C. shasta waterborne spores, exposure durations, and water temperatures. More recent efforts have shown that when coupled with estimates of abundance and temporal migration timing, these tools can be used to predict population-level rates of annual mortality due to ceratomyxosis. In this report, we apply those tools to estimate annual mortality rates of juvenile Coho Salmon Oncorhynchus kisutch originating from the Scott and Shasta rivers that result from exposure to C. shasta in the mainstem Klamath River. Additionally, we simulate how a water management flow regime targeted to reduce disease risk may translate into differing estimates of mortality rates. In general, we found large variation among annual mortality rate estimates, ranging from 0% to 68% across both rivers and across all years considered in this investigation. Further, we estimate that fish from the Shasta River experienced higher mortality rates owning to their prolonged exposure history. Finally, our simulations suggest that the flow regime targeting reduced disease risk could be effective at reducing annual Coho Salmon mortality rate estimates, with the extent of the estimated reductions related to the timing of the onset of measurable in-river waterborne spore concentrations and the overlap with the Klamath River residence for each source population.

California, Oregon↗

USGS2019

Refining the Baseline Sediment Budget for the Klamath River, California

Four dams in the Klamath River Hydroelectric Project (KHP) in Oregon and California (Figure 1) are currently scheduled to be removed over a period of a few weeks or months, beginning in January 2021. The Klamath dam removal will be the largest in the world by almost all measures, and is an unprecedented opportunity to advance science of river responses to such events. The KHP contains approximately 10-12 million cubic meters of mostly fine sediment and model estimates suggest approximately 1/3-2/3 of this volume is expected to be eroded from reservoirs. Much of this sediment is expected to be eventually transported by the river to, or through, the Klamath River Estuary, a distance of more than 300 kilometers. To improve the success of restoration activities following dam removal, agencies must understand the baseline conditions for biological, chemical, and physical processes, prior to the removal. We expect large changes in water quality (turbidity, suspended sediment, dissolved oxygen, temperature, and algal toxins) and in fish habitat in the Hydroelectric Reach and the main-stem of the Klamath River to the ocean. For example, modeled sediment concentrations in the Klamath River during dam removal were estimated exceed 10,000 – 15,000 mg/L, depending on streamflows, location, and the dam removal process, and to remain > 100 – 1000 mg/L for months at a time. Final time to achieve background concentrations post dam removal may take over two years (Reclamation, 2011). Plans to assess many of these changes post-dam removal are still being formulated.

California, Oregon↗

USGS2018

Updates to the suspended sediment SPARROW model developed for western Oregon and northwestern California

A SPARROW (SPAtially Related Regressions On Watershed attributes) model that was previously developed for western Oregon and northwestern California was updated using advancements in the SPARROW software and refinements to the input data. As was the case for the original model calibration, the updated models used the NHD Plus Version 2 as a hydrologic framework and relied on the same estimates of long-term mean suspended-sediment loads and watershed attributes. The updated calibration results indicated that two different SPARROW models were possible—one model from which sediment sources were represented by local lithology and one from which sediment sources were represented by generalized land-cover classes; precipitation, catchment slope, wildfire disturbance, and sediment loss in impoundments were significantly correlated with suspended-sediment loads in both models. The updated models also included a method to compensate for the bias introduced by using total suspended solids to represent suspended sediment in the calibration dataset—a feature that was not available during the original model calibration. The effect of this feature was an overall increase in estimated suspended-sediment loads. Although the lithology- and the land-cover based models used different landscape properties to describe sediment sources, each could be useful in specific applications. The lithology-based model provides more accurate estimates of suspended-sediment load, but the land-cover based model allows water-quality managers to estimate how much in-stream suspended-sediment load originates in areas with extensive development compared to the load that originates in areas with relatively little human impact.

California, Oregon↗

USGS2018

Modeling hydrodynamics, water temperature, and water quality in Klamath Straits Drain, Oregon and California, 2012–15

Executive Summary Located southwest of Klamath Falls, Oregon, Klamath Straits Drain is a 10.1-mile-long canal that conveys water uphill and northward through the use of pumps before discharging to the Klamath River. Klamath Straits Drain traverses an area that historically encompassed Lower Klamath Lake. Currently, the Drain receives water from farmland and from parts of the Lower Klamath Lake National Wildlife Refuge. To support water-quality improvement in Klamath Straits Drain, a hydrodynamic and water-temperature model was constructed and calibrated for calendar years 2012–15 with the two-dimensional model CE-QUAL-W2 (version 4.0). Water quality was calibrated for a subset of that time, from April 1, 2012 to March 31, 2015. Flows in calendar year 2012 were within the normal range, while calendar years 2013–15 were dry years. Significant findings from this study include: In the years studied, only limited flow entered Klamath Straits Drain at the upstream Headworks (KSDH) site. Most flow entered the Drain between KSDH and the E-EE pumps near Township Road through several irrigation channels and ditches. Few data were available to describe the quality of this water for the period of study. The E-EE and F-FF pumps along Klamath Straits Drain mainly operated automatically to keep water levels relatively steady. Ten-minute flow data at streamgage 11509340, downstream of the F-FF pumps, showed high-frequency on/off switching of the F-FF pumps. Combined with daily mean flow data from the F-FF pumps, the downstream 10-minute flow data allowed estimation of 10-minute pumping rates for the F-FF pumps. Paper pump charts showed the existence of short-term variability at the E-EE pumps; however, daily pump data were used at the E-EE pump location in the model. Water temperature in Klamath Straits Drain varied from less than 5 degrees Celsius (°C) (with occasional ice cover in December–January) to greater than 20 °C in May–September. In the years studied, specific conductance was typically 250–850 microsiemens per centimeter, higher than Klamath River specific conductance (typically 100–200 microsiemens per centimeter). Increased chlorophyll a in autumn and winter, along with supersaturated oxygen concentrations, indicated algal blooms in the Drain at that time of year. The blooms were most likely diatoms, based on the timing of blooms sampled elsewhere. Total nitrogen concentration was as much as 5.5 mg/L, with most in dissolved organic and particulate forms, and lower amounts in ammonia and nitrate+nitrite. Total phosphorus concentrations were distributed between orthophophorus (at a median concentration of 0.15 mg/L) and organic and particulate forms (at a median concentration of 0.13 mg/L). Most of the organic carbon in the Klamath Straits Drain was in dissolved rather than particulate form. Newly collected water-quality data for April 1, 2012–March 31, 2015 helped provide the impetus for this modeling study. However, a lack of some data still hindered the construction and calibration of this model. The model would benefit from additional data to describe water-quality boundary conditions, water-quality calibration data upstream of the F-FF pumps, short-term E-EE pump operations, and channel bathymetry in the reach between Highway 97 and the confluence with the Klamath River. Klamath River water mixed upstream into the Klamath Straits Drain, up to the Klamath Straits Drain F-FF pumps at Highway 97, when the F-FF pumps were not operating for periods of hours to days. The F-FF pumps were off for many days during this study, especially during dry years. The boundary between Klamath Straits Drain and the Klamath River was best modeled with an external head condition, which allows exchange of water between the river and the drain in both directions, upstream and downstream. Currently there is a flow gage, water-quality monitor, and a water-quality sampling site located downstream of the F-FF pumps, in the reach where Klamath Straits Drain water can mix with Klamath River water. To sample solely Klamath Straits Drain water, water samples would need to be collected only when the F-FF pumps are actively pumping. Alternately, the sampling location could be moved upstream of the pumps. Interpretation and use of historical water-quality data at the Klamath Straits Drain at Highway 97 site should be done in conjunction with information on pump activity to help inform whether mixing with Klamath River water may have occurred. Total 2014 (a dry year) phosphorus loads from the Drain to the Klamath River were lower and closer to total maximum daily load (TMDL) allocations, as compared to 2013, a year with greater flow and pumping. Modeled travel time through the Klamath Straits Drain, from Headworks to its confluence with the Klamath River, ranged from approximately 24 hours at high flow to 16 days or more, depending on how many days the pumps were turned off. The longer travel times are sufficient for important water-quality transformations, such as algal growth and organic-matter decomposition. This newly constructed model of the Klamath Straits Drain simulates flow, water levels, water temperature, and water quality with acceptable accuracy but with certain data limitations. This model should prove useful in evaluating potential strategies for flow and water-quality management and restoration.

California, Oregon↗

USGS2018

Nutrient loads in the Lost River and Klamath River Basins, south-central Oregon and northern California, March 2012–March 2015

The U.S. Geological Survey and Bureau of Reclamation collected water-quality data from March 2012 to March 2015 at locations in the Lost River and Klamath River Basins, Oregon, in an effort to characterize water quality and compute a nutrient budget for the Bureau of Reclamation Klamath Reclamation Project. The study described in this report resulted in the following significant findings: Total phosphorus (TP), total nitrogen (TN), 5-day biochemical oxygen demand (BOD5), and 5-day carbonaceous biochemical oxygen demand (CBOD5) loads, calculated using the U.S. Geological Survey LOADEST software package at the upper and lower boundaries of the Klamath Reclamation Project, indicated higher loads at the upper boundary on the southern end of Upper Klamath Lake upstream of the Bureau of Reclamation A Canal diversion compared to the lower boundary on the Klamath River downstream of Keno Dam. Accounting for the diversion of loads down A Canal, BOD5 and CBOD5 loads decreased between these two sites during irrigation season, indicating that the Klamath Reclamation Project is not a large source of oxygen-demanding material and that much of the oxygen demand at study site FMT, the northern boundary of the study area, has been expressed by the time the same water passes through site KRK, the southern boundary of the study area. An evaluation of the nutrient balance along the Klamath River flowpath from sites FMT to KRK indicated that, during irrigation season in the 3 years of the study period (March 2012–March 2015), more loads of TP, TN, BOD5, and CBOD5 were being diverted from the Klamath River than were being added to the Klamath River from the combination of Klamath Straits Drain, regulated point sources along the Klamath River, and internal loading from the bottom sediments in the river. By contrast, during non-irrigation seasons, more loads were added to the Klamath River than were diverted through Ady and North Canals, and this difference primarily was due to additional loads to the river from the Lost River Diversion Channel. At the Lost River Diversion Channel, BOD5 loads were higher during irrigation season than non-irrigation season in all three study years owing to the high concentrations of oxygen-demanding cyanobacterial biomass from the seasonal blooms of Aphanizomenon flos-aquae in the Klamath River and Upper Klamath Lake. The difference between the two seasons was particularly large in years 2 and 3, when the low flows of these two drought years resulted in smaller nonirrigation period loads than in year 1. CBOD5 loads also were higher during irrigation season in years 2 and 3 than during non-irrigation season, indicating that the largest oxygen demand was coming from senescence of Aphanizomenon flos-aquae cells that are present in the Klamath River during the summer. However, during irrigation season in year 1, CBOD5 loads were lower than in the non-irrigation season, which may indicate that at times high concentrations of ammonia or cellular organic nitrogen leaving Upper Klamath Lake contribute a large nitrogenous oxygen demand as well. The smallest loads were computed for the farthest upstream sites in the Lost River Basin, suggesting that the upper Lost River Basin does not contribute substantial loads of TP, TN, BOD5, and CBOD5 to the Klamath Reclamation Project. Median concentrations of BOD5 and CBOD5 were lowest among the upper Lost River Basin sites and highest at site PPD (however, this comparison is based on only four samples collected at site PPD over the 3-year study). Median concentrations of BOD5 and CBOD5 also were elevated at sites KSDH (6.60 and 4.70 milligrams per liter [mg/L], respectively) and KSD97 (4.47 and 3.45 mg/L, respectively). The highest maximum BOD5 and CBOD5 concentrations were reported at the Lost River Diversion Channel (39.0 and 26.5 mg/L, respectively) when water was flowing from the Klamath River toward the Klamath Reclamation Project, and site FMT (25.0 and 23.9 mg/L, respectively), the study site at the southern end of Upper Klamath Lake. Carbonaceous oxygen demand, as represented by CBOD5, typically dominated the composition of the samples at all sites. The highest concentrations of dissolved organic carbon were present at sites KSDH (the headworks of Klamath Straits Drain) and KSD97 (Klamath Straits drain before it enters the Klamath River), and PPD (outlet of Tule Lake). Median concentrations of TN and TP at the upper Lost River Basin sites in years 1 and 2 were variable, but site MCRV showed a smaller range of values in those years compared to the other upper Lost River Basins sites, and an overall lower median concentration during irrigation seasons in years 1 and 2, suggesting that Gerber Reservoir does not contribute high concentrations of nutrients to the Lost River during irrigation season. Total Maximum Daily Load (TMDL) load allocations for TP and TN in Klamath Straits Drain were exceeded in all three study years. BOD5 load allocations were exceeded in years 1 and 2, but not year 3. TMDL load allocations for TP were exceeded in the Lost River Diversion Channel for all 3 years. Load allocations for TN were exceeded in year 1, but not in years 2 and 3. BOD5 loads were less than the TMDL load allocation for all three study years. The dearth of samples collected at the Klamath Straits Drain just downstream of the Lower Klamath National Wildlife Refuge did not allow for direct assessment of the Klamath Straits Drain acting as a nutrient source or sink. TP, TN, BOD5, and CBOD5 loads estimated during the study period likely were smaller than long-term average conditions because of persistent drought conditions in the Upper Klamath Basin. The study results, therefore, fail to characterize loads from the Klamath Reclamation Project to the Klamath River that could be present in typical years, and suggest the need for load assessments during average or aboveaverage streamflow years.

California, Oregon↗

USGS2018

Klamath River Basin water-quality data

The Klamath River Basin stretches from the mountains and inland basins of south-central Oregon and northern California to the Pacific Ocean, spanning multiple climatic regions and encompassing a variety of ecosystems. Water quantity and water quality are important topics in the basin, because water is a critical resource for farming and municipal use, power generation, and for the support of wildlife, aquatic ecosystems, and endangered species. Upper Klamath Lake is the largest freshwater lake in Oregon (112 square miles) and is known for its seasonal algal blooms. The Klamath River has dams for hydropower and the upper basin requires irrigation water to support agriculture and grazing. Multiple species of endangered fish inhabit the rivers and lakes, and the marshes are key stops on the Pacific flyway for migrating birds. For these and other reasons, the water resources in this basin have been studied and monitored to support their management distribution.

California, Oregon↗

USGS2018

Juvenile Lost River and shortnose sucker year class strength, survival, and growth in Upper Klamath Lake, Oregon, and Clear Lake Reservoir, California—2016 Monitoring Report

Executive Summary 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.

California, Oregon↗

USGS2017

Characteristics of dissolved organic matter in the Upper Klamath River, Lost River, and Klamath Straits Drain, Oregon and California

Concentrations of particulate organic carbon (POC) and dissolved organic carbon (DOC), which together comprise total organic carbon, were measured in this reconnaissance study at sampling sites in the Upper Klamath River, Lost River, and Klamath Straits Drain in 2013–16. Optical absorbance and fluorescence properties of dissolved organic matter (DOM), which contains DOC, also were analyzed. Parallel factor analysis was used to decompose the optical fluorescence data into five key components for all samples. Principal component analysis (PCA) was used to investigate differences in DOM source and processing among sites. At all sites in this study, average DOC concentrations were higher than average POC concentrations. The highest DOC concentrations were at sites in the Klamath Straits Drain and at Pump Plant D. Evaluation of optical properties indicated that Klamath Straits Drain DOM had a refractory, terrestrial source, likely extracted from the interaction of this water with wetland peats and irrigated soils. Pump Plant D DOM exhibited more labile characteristics, which could, for instance, indicate contributions from algal or microbial exudates. The samples from Klamath River also had more microbial or algal derived material, as indicated by PCA analysis of the optical properties. Most sites, except Pump Plant D, showed a linear relation between fluorescent dissolved organic matter (fDOM) and DOC concentration, indicating these measurements are highly correlated (R 2 =0.84), and thus a continuous fDOM probe could be used to estimate DOC loads from these sites.

California, Oregon↗

USGS2017

Emplacement of Holocene silicic lava flows and domes at Newberry, South Sister, and Medicine Lake volcanoes, California and Oregon

This field guide for the International Association of Volcanology and Chemistry of the Earth’s Interior (IAVCEI) Scientific Assembly 2017 focuses on Holocene glassy silicic lava flows and domes on three volcanoes in the Cascade Range in Oregon and California: Newberry, South Sister, and Medicine Lake volcanoes. Although obsidian-rich lava flows have been of interest to geologists, archaeologists, pumice miners, and rock hounds for more than a century, many of their emplacement characteristics had not been scientifically observed until two very recent eruptions in Chile. Even with the new observations, several eruptive processes discussed in this field trip guide can only be inferred from their final products. This makes for lively debates at outcrops, just as there have been in the literature for the past 30 years. Of the three volcanoes discussed in this field guide, one (South Sister) lies along the main axis defined by major peaks of the Cascade Range, whereas the other two lie in extensional tectonic settings east of the axis. These two tectonic environments influence volcano morphology and the magmatic and volcanic processes that form silicic lava flows and domes. The geomorphic and textural features of glass-rich extrusions provide many clues about their emplacement and the magma bodies that fed them. The scope of this field guide does not include a full geologic history or comprehensive explanation of hazards associated with a particular volcano or volcanic field. The geochemistry, petrology, tectonics, and eruption history of Newberry, South Sister, and Medicine Lake volcanic centers have been extensively studied and are discussed on other field excursions. Instead, we seek to explore the structural, textural, and geochemical evolution of well-preserved individual lava flows—the goal is to understand the geologic processes, rather than the development, of a specific volcano.

California, Oregon↗

USGS2016

Ground squirrel shooting and potential lead exposure in breeding avian scavengers

Recreational ground squirrel shooting is a popular activity throughout the western United States and serves as a tool for managing ground squirrel populations in agricultural regions. Belding’s ground squirrels ( Spermophilus beldingi ) are routinely shot in California, Nevada, and Oregon across habitats that overlap with breeding avian scavengers. Ground squirrels shot with lead (Pb)-based bullets may pose a risk to avian scavengers if they consume carcasses containing Pb fragments. To assess the potential risk to breeding avian scavengers we developed a model to estimate the number, mass, and distribution of Pb fragments in shot ground squirrels using radiographic images. Eighty percent of shot carcasses contained detectible Pb fragments with an average of 38.6 mg of Pb fragments. Seven percent of all carcasses contained Pb fragment masses exceeding a lethal dose for a model raptor nestling (e.g. American kestrel Falco sparverius ). Bullet type did not influence the number of fragments in shot ground squirrels, but did influence the mass of fragments retained. Belding’s ground squirrels shot with .17 Super Mag and unknown ammunition types contained over 28 and 17 times more mass of Pb fragments than those shot with .22 solid and .22 hollow point bullets, respectively. Ground squirrel body mass was positively correlated with both the number and mass of Pb fragments in carcasses, increasing on average by 76% and 56% respectively across the range of carcass masses. Although the mass of Pb retained in ground squirrel carcasses was small relative to the original bullet mass, avian scavenger nestlings that frequently consume shot ground squirrels may be at risk for Pb-induced effects (e.g., physiology, growth, or survival). Using modeling efforts we found that if nestling golden eagles ( Aquila chrysaetos ), red-tailed hawks ( Buteo jamaicensis ), and Swainson’s hawks ( B . swainsoni ) consumed shot ground squirrels proportionately to the nestling’s mass, energy needs, and diet, 100% of the nestling period would exceed a 50% reduction in delta-aminolevulinic acid dehydratase production threshold, the last 13–27% of the nestling stage would exceed a reduced growth rate threshold, but no nestlings would be expected to exceed a level of Pb ingestion that would be lethal.

California, Oregon↗

USGS2016

Colonial waterbird predation on Lost River and Shortnose suckers in the Upper Klamath Basin

We evaluated predation on Lost River Suckers Deltistes luxatus and Shortnose Suckers Chasmistes brevirostris by American white pelicans Pelecanus erythrorhynchos and double-crested cormorants Phalacrocorax auritus nesting at mixed-species colonies in the Upper Klamath Basin of Oregon and California during 2009–2014. Predation was evaluated by recovering (detecting) PIT tags from tagged fish on bird colonies and calculating minimum predation rates, as the percentage of available suckers consumed, adjusted for PIT tag detection probabilities but not deposition probabilities (i.e., probability an egested tag was deposited on- or off-colony). Results indicate that impacts of avian predation varied by sucker species, age-class (adult, juvenile), bird colony location, and year, demonstrating dynamic predator–prey interactions. Tagged suckers ranging in size from 72 to 730 mm were susceptible to cormorant or pelican predation; all but the largest Lost River Suckers were susceptible to bird predation. Minimum predation rate estimates ranged annually from <0.1% to 4.6% of the available PIT-tagged Lost River Suckers and from <0.1% to 4.2% of the available Shortnose Suckers, and predation rates were consistently higher on suckers in Clear Lake Reservoir, California, than on suckers in Upper Klamath Lake, Oregon. There was evidence that bird predation on juvenile suckers (species unknown) in Upper Klamath Lake was higher than on adult suckers in Upper Klamath Lake, where minimum predation rates ranged annually from 5.7% to 8.4% of available juveniles. Results suggest that avian predation is a factor limiting the recovery of populations of Lost River and Shortnose suckers, particularly juvenile suckers in Upper Klamath Lake and adult suckers in Clear Lake Reservoir. Additional research is needed to measure predator-specific PIT tag deposition probabilities (which, based on other published studies, could increase predation rates presented herein by a factor of roughly 2.0) and to better understand biotic and abiotic factors that regulate sucker susceptibility to bird predation.

California, Oregon↗

USGS2016

Genetic diversity and population structure in the threatened Oregon silverspot butterfly ( Speyeria zerene hippolyta ) in western Oregon and northwestern California— Implications for future translocations and the establishment of new populations

Executive Summary We present results of population genetic analyses performed on Oregon silverspot butterflies (OSB; Speyeria zerene hippolyta ) in western Oregon and northwestern California. We used DNA sequences from a 561-base pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene for a dataset comprised of 112 S. z. hippolyta and 32 S. z. gloriosa individuals collected at 9 locations in western Oregon and northwestern California. The most pertinent findings thus far are summarized as follows: Among OSB populations, genetic diversity is lowest at Mount Hebo and highest at Rock Creek and Bray Point. Of the 32 haplotypes detected in OSB, only 2 were shared among populations (1 shared by Mount Hebo, Cascade Head, Bray Point, and Rock Creek, and 1 shared by Rock Creek and Lake Earl). The remaining 30 haplotypes were identified in individual populations, highlighting the strong differentiation among sites. It is unclear if the shared haplotypes represent widespread, naturally occurring genetic variation or if allele sharing among populations is due to translocation history. Using full siblings of individuals that were released at Rock Creek and Bray Point in 2012 as comparison standards, the analyses suggest that 54 percent of the sampled individuals from Bray Point were naturally recruited into the population and were not originating from the 2012 release of captive reared individuals. Likewise, 33 percent of the analyzed individuals from Rock Creek were naturally recruited. Both of these estimates may be underestimates if the shared alleles that we identified among populations are naturally occurring and not a product of the 2012 translocations. The results suggest that there are about 12–13 COI haplotypes in the Mount Hebo population. The U.S. Fish and Wildlife Service anticipates using Mount Hebo as the source of individuals when establishing new populations in the future. Nonlinear regression models based on a series of rarefaction analyses suggest that progeny from 12, 37, 109, and 326 female individuals would be required to respectively capture 25, 50, 75, and 90 percent of the allelic diversity from Mount Hebo. Phylogenetic analyses identified two different haplotype groups, but the two groups did not correspond to the different subspecies used in the analysis. One group included 22 S. z. hippolyta haplotypes and 7 haplotypes identified in S. z. gloriosa . The second group included eight haplotypes from S. z. hippolyta, three haplotypes from S. z. gloriosa , and one haplotype that was detected in both subspecies.

California, Oregon↗

USGS2016

Life history diversity in Klamath River steelhead

Oncorhynchus mykiss exhibits a vast array of life histories, which increases its likelihood of persistence by spreading risk of extirpation among different pathways. The Klamath River basin (California–Oregon) provides a particularly interesting backdrop for the study of life history diversity in O. mykiss , in part because the river is slated for a historic and potentially influential dam removal and habitat recolonization project. We used scale and otolith strontium isotope ( 87 Sr/ 86 Sr) analyses to characterize life history diversity in wild O. mykiss from the lower Klamath River basin. We also determined maternal origin (anadromous or nonanadromous) and migratory history (anadromous or nonanadromous) of O. mykiss and compared length and fecundity at age between anadromous (steelhead) and nonanadromous (Rainbow Trout) phenotypes of O. mykiss . We identified a total of 38 life history categories at maturity, which differed in duration of freshwater and ocean rearing, age at maturation, and incidence of repeat spawning. Approximately 10% of adult fish sampled were nonanadromous. Rainbow Trout generally grew faster in freshwater than juvenile steelhead; however, ocean growth afforded adult steelhead greater length and fecundity than adult Rainbow Trout. Although 75% of individuals followed the migratory path of their mother, steelhead produced nonanadromous progeny and Rainbow Trout produced anadromous progeny. Overall, we observed a highly diverse array of life histories among Klamath River O. mykiss . While this diversity should increase population resilience, recent declines in the abundance of Klamath River steelhead suggest that life history diversity alone is not sufficient to stabilize a population. Our finding that steelhead and Rainbow Trout give rise to progeny of the alternate form (1) suggests that dam removal might lead to a facultatively anadromous O. mykiss population in the upper basin and (2) raises the question of whether both forms of O. mykiss in the Klamath River should be managed under the same strategy.

California, Oregon↗

USGS2016

Post-release survival and movement of Western Grebes ( Aechmophorus occidentalis ) implanted with intracoelomic satellite transmitters

The main goal of this study was to gain knowledge on post-release survival and movement of Western Grebes ( Aechmophorus occidentalis ) using a modified technique for implanting satellite transmitters. This technique had improved post-surgical survival in an earlier study. Nine Western Grebes, implanted with intracoelomic (within the body cavity) satellite transmitters with percutaneous antennae, were released close to their capture site in San Francisco Bay, California, USA. Eight survived at least 25 days (average number of transmittal days was 140.8), while two had transmitters that provided data for greater than 1 year (436 and 454 days). The average cumulative distance recorded for all Western Grebes ( n = 9) was 829 km with two round-trip movements documented. One individual Western Grebe traveled a cumulative round-trip distance of 2,144 km in July and November 2011, while another individual traveled a round-trip distance of 1,514 km between 8 and 14 December 2011. This study provides a step forward in testing implantable satellite transmitters in Western Grebes and highlights the need to further improve tracking methods, potentially improving our understanding of their population threats.

California, Oregon↗

USGS2016

Potential effects of sea-level rise on plant productivity: Species-specific responses in northeast Pacific tidal marshes

Coastal wetland plants are adapted to varying degrees of inundation. However, functional relationships between inundation and productivity are poorly characterized for most species. Determining species-specific tolerances to inundation is necessary to evaluate sea-level rise (SLR) effects on future marsh plant community composition, quantify organic matter inputs to marsh accretion, and inform predictive modeling of tidal wetland persistence. In 2 macrotidal estuaries in the northeast Pacific we grew 5 common species in experimental mesocosms across a gradient of tidal elevations to assess effects on growth. We also tested whether species abundance distributions along elevation gradients in adjacent marshes matched productivity profiles in the mesocosms. We found parabolic relationships between inundation and total plant biomass and shoot counts in Spartina foliosa and Bolboschoenus maritimus in California, USA, and in Carex lyngbyei in Oregon, USA, with maximum total plant biomass occurring at 38, 28, and 15% time submerged, respectively. However, biomass of Salicornia pacifica and Juncus balticus declined monotonically with increasing inundation. Inundation effects on the ratio of belowground to aboveground biomass varied inconsistently among species. In comparisons of field distributions with mesocosm results, B. maritimus , C. lyngbyei and J. balticus were abundant in marshes at or above elevations corresponding with their maximum productivity; however, S. foliosa and S. pacifica were frequently abundant at lower elevations corresponding with sub-optimal productivity. Our findings show species-level differences in how marsh plant growth may respond to future SLR and highlight the sensitivity of high marsh species such as S. pacifica and J. balticus to increases in flooding.

California, Oregon↗