Geology topics

Carl O. Ostberg

Publications and source records attributed to Carl O. Ostberg.

At least 19 recordsLinked to original sources

USGS2026

Tracking Pacific salmon migrations with a prototype eDNA autosampler

Pacific salmon ( Oncorhynchus spp.) are keystone species that support commercial and recreational fisheries and play a significant role in Indigenous cultures. As a keystone species, they are commonly monitored to assess population metrics and adult and juvenile migration. Environmental DNA (eDNA) has been successfully applied to salmon monitoring, but these efforts have relied on manually collected samples which can limit temporal resolution and increase field effort. Here, we evaluated a prototype autonomous eDNA sampler for fine-scale tracking of adult salmon migrations in the Lake Washington Ship Canal (LWSC) in Washington state, USA. The autosampler was deployed approximately 3 km upstream of the Ballard Locks, where returning adult salmon are counted daily, for 4 months during the adult salmon return in 2022, and it collected eDNA samples twice daily (day and night) onto self-preserving filters. We tested eDNA samples for Chinook Salmon ( Oncorhynchus tshawytscha ), Sockeye Salmon ( O. nerka ) and Coho Salmon ( O. kisutch ) and results were compared with daily adult counts at the Ballard Locks. eDNA detection lagged visual counts by approximately 5 days for Sockeye and Coho salmon and approximately 23 days for Chinook Salmon. The extensive time lag in eDNA detection for Chinook Salmon was likely due to a thermal barrier, delaying their migration through the LWSC. We found no clear effect of day versus night sampling on eDNA detection probability. Two additional experiments were performed: one to assess eDNA degradation on used self-preserving filters stored in the autosampler and another to assess whether our 3 L system flush volume was sufficient to prevent residual eDNA from being carried over from one sample to the next. We found no apparent eDNA degradation but potential for sample-to-sample carry over at this flush volume. Our study highlights the need to consider strategic placement of the autosampler intake to optimize eDNA capture and testing of flush volumes to minimize sample-to-sample carryover. Autonomous eDNA sampling provided efficient, high-frequency, and fine-scale surveillance of salmon migrations and offers a scalable approach for a wide variety of monitoring applications.

Washington↗

USGS2026

Poor population recovery of Lake Washington Chinook Salmon (Oncorhynchus tshawytscha) in Pacific Northwestern USA may be associated with disease caused by Ceratonova shasta in an urban-influenced watershed

Understanding the effects of anthropogenic changes on fish disease is vital for supporting mitigative actions for fisheries population recovery. The Lake Washington watershed in the Pacific Northwestern United States is influenced by high urban development and climate change, compromising the sustainability of anadromous salmon. We investigated Ceratonova shasta , a myxozoan parasite, in Chinook Salmon Oncorhynchus tshawytscha to determine the impacts of C. shasta -induced enteronecrosis during salmon freshwater migrations within this watershed. All sampled adult Chinook Salmon returning to an enhancement hatchery to spawn were infected with genotype I C. shasta with a high prevalence of severe enteritis and enteronecrosis. Parasite loads and associated pathology were more severe in adult fish succumbing to prespawn mortality than in fish that spawned. Natural prespawn mortality of Chinook Salmon in the Cedar River was also associated with high C. shasta loads. Sentinel exposure studies with Chinook Salmon juveniles in the spring and fall demonstrated high levels of C. shasta genotype II actinospores in the Lake Washington Ship Canal, a human engineered canal that salmon must traverse in their freshwater migrations from the Puget Sound. The sentinel juvenile Chinook Salmon succumbed to clinical disease and high mortality from genotype II C. shasta , suggesting that these stocks have high susceptibility to this genotype. The results show that both genotypes I and II pose disease risks to adult and juvenile stages of Chinook Salmon in the watershed, and that the Lake Washington Ship Canal could be a C. shasta ‘hot spot’ for genotype II that may increase disease risk for juveniles during smolt emigration.

Washington↗

USGS2026

Unveiling a legacy of fish introductions to mountain lakes using historical records and eDNA surveys in a National Park

Across the western United States, introductions of non-native fish into historically fishless mountain lakes have impacted native biota. Understanding the impacts of fish introductions is essential for conservation in Olympic National Park, a Biosphere Reserve. We reconstructed fish plantings using records dating back to 1930, followed by environmental DNA (eDNA) surveys to estimate the current distribution of fish and amphibians in 117 remote mountain lakes. We used Bayesian multiscale occupancy models to determine how lake attributes and planting history related to fish and amphibian occupancy. The most frequently detected species were Brook Trout, Rainbow Trout, Cascades Frog, and Northwestern Salamander. eDNA sampling revealed 52 lakes with amphibians only, 45 with fish and amphibians, 14 with fish only, and 6 unoccupied. Of the 53 lakes with planting records, 38 had fish eDNA detected. Fish eDNA was also detected in 21 lakes lacking planting records, which could reflect incomplete records, unauthorized plantings, and false positive detections. Of the three species planted, Cutthroat Trout had the highest failure rate and did not become established in 23 of 28 historically planted lakes. In a subset of 9 lakes sampled for up to 7 years, those with known fish and amphibian presence showed consistent eDNA detections over time. The number of times a lake was stocked was the best predictor of occupancy for Brook and Rainbow trout, while higher occupancy for Brook Trout was also associated with lower elevations, lower solar radiation, and larger lake area. We did not observe widespread negative associations between amphibian occupancy and fish presence, although there was a negative relationship between fish presence and Rough-skinned Newt and Long-toed Salamander occupancy. Cascades Frog occupancy showed no relationship to fish presence or lake traits. Our results suggest mechanisms of fish persistence over time and highlight areas where native amphibians are impacted by introduced fish. These results can guide management options like targeted fish removals that benefit native fauna while still supporting recreational fishing. More broadly, our work demonstrates the value of combining historical records with contemporary surveys and the utility of eDNA for broad-scale surveys of species distribution in remote wilderness areas.

Washington↗

USGS2025

A molecular specimen bank for contemporary and future study captures landscape-scale biodiversity baselines before Klamath River dam removal

Global restoration and conservation of freshwater biodiversity are represented in practice by works such as the Klamath River Renewal Project (KRRP), the largest dam removal and river restoration in the United States, which has reconnected 640 river kilometers. With dam removals, many biological outcomes remain understudied due to a lack of pre-impact data and complex ecosystem recovery timeframes. To avoid this, we created the KRRP molecular library, an environmental specimen bank, for long-term curation of environmental nucleic acids collected from the restoration project. We used these initial samples, environmental DNA metabarcoding, and generalized linear mixed-effects models to evaluate patterns of pre-dam removal fish richness and diversity. Demonstrating the suitability to resolve biological differences, the baseline shows that tributary and mainstem streams had greater native fish diversity and 2.3–10.7 times greater native fish species richness than reservoirs. These and future sampling efforts should, at a minimum, allow tracking of fish community response to ecosystem restoration. Anticipating the acceleration of omics innovation, we preserved samples for long-term storage and identified requisite phases for sustained function and adaptation of the molecular library: securing a physical storage facility for genetic material, establishing a governance structure, and confirming support for archive management.

California, Oregon↗

USGS2024

Using environmental DNA to assess the response of steelhead/Rainbow Trout and Coastrange Sculpin populations to postfire debris flows in coastal streams of Big Sur, California

Objective Debris flows are among the most extreme disturbances to streams and are predicted to become more frequent under climate change. We assessed the response of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout)/Rainbow Trout (hereafter, collectively referred to as O. mykiss ) and Coastrange Sculpin Cottus aleuticus populations to major postfire debris flows in two small coastal basins of California using noninvasive environmental DNA (eDNA) sampling. Methods We analyzed water samples from disturbed reaches for eDNA in the first two summers after debris flows. In Big Creek, all Coastrange Sculpin habitat was disturbed by debris flows, but a major tributary occupied by O. mykiss was not affected. In Mill Creek, all available habitat for both species was disturbed. We also sampled two unburned basins as undisturbed reference streams. Result In Big Creek, O. mykiss eDNA was detected in all water samples during both years, and concentrations in some samples approached the lowest concentrations in the reference streams. Coastrange Sculpin eDNA was detected only in a single water sample in the first year and was not detected in the second year. In Mill Creek, neither species was detected in the first year, but during the second year, O. mykiss eDNA was detected at very low concentrations in 40% of samples and Coastrange Sculpin eDNA was detected in a single sample. Conclusion Our results indicate that O. mykiss and Coastrange Sculpins either survived in or quickly reoccupied the disturbed reaches from within the basins. However, the detection rates for cases in which all habitat for a species in a basin was affected by debris flows indicate that abundances were very low, suggesting that persistence may be uncertain unless there is successful reproduction or immigration. Finally, eDNA appears to be effective for monitoring sensitive fish populations after a major disturbance; however, detection rates in individual samples may be low and require appropriate sampling designs to achieve the desired detection probability.

California↗

USGS2024

Shift in piscivory by salmonids following invasion of a minnow in an oligotrophic reservoir

Predation can play an important role in structuring ecological communities, and predator–prey dynamics can be altered following the introduction of new species. An unauthorized introduction of redside shiner ( Richardsonius balteatus ) into reservoirs in the Upper Skagit River, Washington, USA created concern that a consequent shift in predator–prey dynamics in the reservoirs could reduce recruitment and production of native salmonids in the basin. We estimated predation mortality in Ross Lake on nonnative redside shiner and juvenile native salmonids to evaluate the potential role of predation in regulating these populations and limiting survival of native species of concern. We used bioenergetics modelling and stable isotope analysis combined with directed field measurements of growth, seasonal diet and thermal experience of piscivorous salmonids to quantify their consumption demand on prey fishes to evaluate the relative magnitude of predation mortality on invasive redside shiners and native salmonids. While redside shiner are the dominant prey fish species in Ross Lake, the modest biomass of native salmonids consumed could translate into substantial mortality, the magnitude of which depended on the timing and size at which prey fishes were eaten. This information provides important context for how nonnative species may indirectly impact native species through shared predation (apparent competition) and can inform conservation decisions surrounding nonnative species control, sustainability of native salmonids and introductions of anadromous fishes.

Ecology of Freshwater Fish↗

USGS2024

Spatial and temporal surveys of salmon environmental DNA (eDNA) in a Seattle urban creek

Seattle Public Utilities (SPU) has a history of conducting traditional fish surveys in urban streams of Seattle, Washington. Limited staff resources have reduced SPU's capacity to monitor fish, and environmental DNA (eDNA) was recognized as an alternative survey method that could potentially improve the efficiency and capacity of SPU-sponsored fish surveys. We performed spatiotemporal surveys of eDNA to assess occupancy and distribution of Chinook Salmon ( Oncorhynchus tshawytscha ), Coho Salmon ( O . kisutch ), and Coastal Cutthroat Trout ( O . clarkii clarkii ) in Thornton Creek, Seattle, between October 2018 and December 2020. Peak Chinook and Coho eDNA detections occurred in October and October–November, respectively, coinciding with expected adult return time. Chinook and Coho eDNA was detected in May at the time when juveniles outmigrate through the Lake Washington basin. Coastal Cutthroat Trout eDNA was widespread and detected at high rates across seasons, reflecting their ubiquitous distribution. Results from multiscale occupancy modeling suggested that distance upstream affected site-level occupancy probabilities for adult Chinook, but not Coho. Model results also suggested that the probability of Coho and Chinook eDNA occurring in water samples was affected by survey year. Finally, model results suggested that the probability of detecting Chinook eDNA in PCR technical replicates was affected by survey year and collection day but detection of Coho eDNA was only affected by collection day. This study indicates eDNA surveys are effective for assessing distribution and occupancy of salmonids in Seattle's urban streams. Integrating eDNA surveys into urban stream monitoring programs can help alleviate the burden of limited assets facing many resource managers.

Washington↗

USGS2023

Growth performance of Rainbow Trout in reservoir tributaries and implications for steelhead growth potential above Skagit River dams

Objective In the Pacific Northwest (USA), Pacific salmon Oncorhynchus spp. populations have been declining significantly for decades, prompting stakeholders to respond with a variety of conservation and restoration measures. One such measure being considered in the Skagit River basin (Washington, USA) is the introduction of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) above the impassable Gorge, Diablo, and Ross dams to bolster their populations. Because freshwater growth is key to survival at subsequent life stages, we evaluated current trends in size and growth of Rainbow Trout among key tributaries to Gorge, Diablo, and Ross reservoirs using empirical data collection and bioenergetics modeling. Methods For nine candidate streams, a bioenergetics model was used to assess how temperature and prey consumption affected growth performance of Rainbow Trout between annuli 1 and 2, and 2 and 3. Thermal scenarios were created to evaluate how fish growth responded to temperature variability while total annual consumption was constrained within empirical growth estimates. We then compared these results to back-calculated size thresholds established by size-at-age observed in wild steelhead adults that returned to the Skagit River below the dams. Result Of the streams proposed for introductions, there was one instance (McMillan Creek) in the nominal simulations where growth met or exceeded the size at annulus 2 or 3 of a returning adult steelhead (24.9 g at annulus 2 and 50.3 g at annulus 3). Modeled growth under different thermal scenarios showed that colder temperatures (0.1–10.7°C, Canyon Creek) produced higher growth than under the nominal or warm scenarios (2.0–15.3°C, Canyon Creek), as well as one additional tributary where size at annulus 2 or 3 (±2 SE) was comparable to the threshold established by adult steelhead below the dams (Big Beaver Creek, annulus 3). Conclusion These results suggest Rainbow Trout growth is most limited by prey availability in the examined upper Skagit tributaries.

Washington↗

USGS2023

Development of a quantitative PCR assay for detecting northwest salamander (ambystoma gracile) in environmental DNA samples

We developed a primer and probe based quantitative PCR assay for use with environmental DNA to detect Northwest salamander ( Ambystoma gracile ), a species endemic to the temperate Pacific coastal region of North America. The assay targets a region in the mitochondrial DNA (mtDNA) D-loop gene. Tests of the assay were performed in silico (using the NCBI BLAST tool), in vitro (using DNA extracted from A. gracile and related species) and in situ (water samples collected from a lake with a known population of A. gracile ). This assay will be useful in efforts to monitor the distribution and occupancy of this species.

Conservation Genetics Resources↗

USGS2022

Risk assessment for bull trout introduction into Sullivan Lake and Harvey Creek, northeastern Washington

The Kalispel Tribe of Indians (KT), U. S. Fish and Wildlife Service, and Washington Department of Fish and Wildlife are engaged in conservation of bull trout ( Salvelinus confluentus ) in the Lake Pend Oreille (LPO) Core Area. The LPO is a complex habitat core area which falls within three states (Montana, Idaho, and Washington) and a tribal entity. As part of the conservation process, KT worked in cooperation with the U. S. Geological Survey (USGS) to complete a risk assessment for introduction of bull trout into Sullivan Lake/Harvey Creek, northeastern, Washington. The risk assessment was designed to evaluate potential risks to resident fish species, to bull trout introduced into Sullivan Lake, and to bull trout donor source populations. This risk assessment describes the potential risks associated with pathogens (introduction of pathogens and increased pathogen burden), genetics (such as risk to donor sources, straying and breeding with native bull trout, and introduction of bull-brook hybrids), and ecological interactions (such as predation and competition). Potential donor source populations were identified and evaluated using a qualitative approach based on expert opinion and a decision framework. Literature reviews were completed for fish species composition and abundance in Sullivan Lake basin to assess potential ecological interactions and risks to these populations and to the introduced bull trout. The USGS assessed pathogen risks through two major questions: (1) whether introduced bull trout might bring pathogens into the Sullivan Lake basin that were not previously present and (2) whether the health of introduced bull trout could be adversely affected by pathogens already present in the basin. Assessment of genetic risks included demographic risks to donor source populations, potential for hybridization with native bull trout, and the risk of introducing bull-brook hybrids. Literature reviews were used in conjunction with discussions among regional biologists to identify potential donor source populations and their population attributes. A decision framework was developed by USGS in collaboration with KT biologists that identified desirable population attributes (life history behavior, abundance, population viability, feasibility of collection, and environmental match) associated with donor source populations and established ranking criteria. The population attribute information was used with the (1) decision framework, (2) established ranking criteria, and (3) expert opinion of regional biologists, to assign scores for overall ranking of donor source populations. The LPO source population was the highest ranked and is considered a robust and stable population. The risk of introducing pathogens from LPO into Sullivan Lake via a bull trout introduction program seems low, and indirect pathogen burden risks to resident species can be mitigated using established pathogen surveillance methods. The likelihood that bull trout, introduced into Sullivan Lake, stray and spawn with native bull trout is low. Nearest-neighbor donor source populations, such as LPO, could minimize negative fitness impacts that might occur from straying and interbreeding of individuals that become entrained and help maintain natural patterns of genetic diversity in native populations. The ecological risk that a bull trout introduction presents to resident species seems to be low but with some uncertainty. Pygmy whitefish, a Washington State Sensitive species, is likely most vulnerable to extirpation with increased predation pressure with introduction of an additional piscivore into the ecosystem. The status of the pygmy whitefish in Sullivan Lake is unknown. The ecological risks most likely to reduce the viability of introduced bull trout are predation by burbot and an adequate forage base in Sullivan Lake. Prior fish surveys provided data on resident species abundance, provided an established baseline for effective monitoring, and identifying ecosystem changes post-bull trout introduction to inform future adaptive management decisions.

Washington↗

USGS2021

Growth, survival, and cohort formation of juvenile Lost River (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) in Upper Klamath Lake, Oregon, and Clear Lake Reservoir, California—2019 Monitoring Report

Populations of federally endangered Lost River ( Deltistes luxatus ) and shortnose suckers ( Chasmistes brevirostris ) in Upper Klamath Lake, Oregon, and Clear Lake Reservoir (hereinafter, Clear Lake), California, are experiencing long-term decreases in abundance. Upper Klamath Lake populations are decreasing not only due to adult mortality, which is relatively low, but also because they are not being balanced by recruitment of young adult suckers into known adult spawning aggregations. Long-term monitoring of juvenile sucker populations is conducted to (1) determine if there are annual and species-specific differences in production, survival, and growth, (2) better understand when juvenile sucker mortality is greatest, and (3) help identify potential causes of high juvenile sucker mortality particularly in Upper Klamath Lake. The U.S. Geological Survey monitoring program, that began in 2015, tracks cohorts through summer months and among years in Upper Klamath and Clear Lakes. Data on juvenile suckers captured in trap nets are used to provide information on annual variability in age-0 sucker apparent production, juvenile sucker apparent survival, apparent growth, species composition, and health. Upper Klamath Lake indices of year-class strength indicated that the 2019 year-class was the strongest in the past 5 years of monitoring. Low detections of age-1 and older suckers indicate that the 2018 cohort experienced poor survival within the first year of life. Shortnose suckers constituted the smallest proportion and suckers with uncertain species identification constituted the largest proportion of the 2019 year-class. Small numbers of Lost River sucker were captured consistently throughout the sampling season. The relative abundance of age-0 suckers is not a good indicator of year-class strength in Clear Lake. There were no age-0 suckers captured in Clear Lake during the 2015 and 2019 sampling seasons. Most suckers captured were age-1 Klamath largescale/shortnose suckers, which indicated a relatively strong 2018 cohort. Four-year old juveniles from the 2015 cohort were present in 2019 in Clear Lake. Cohorts that do not recruit to our sampling gear until a year or more of age seem to indicate that (1) a stream resident life history is contributing to the lake population and (2) juvenile suckers occupy the Willow Creek drainage for a full year or more. Although these suckers could be either the non-endangered Klamath largescale or the endangered shortnose suckers, a stream resident life history is consistent with these fish being Klamath largescale suckers. Survival of all distinguishable taxa of juvenile suckers is much higher in Clear Lake than in Upper Klamath Lake, with non-trivial numbers of suckers surviving to join spawning aggregations in most years.

California, Oregon↗

USGS2021

Ontogeny of eDNA shedding during early development in Chinook Salmon (Oncorhynchus tshawytscha)

Knowledge of the timing of major life history events in aquatic species is important for informing conservation and resource management planning. Accordingly, surveys of environmental DNA (eDNA) have been performed to determine the efficacy of eDNA for providing information on life history events, primarily focusing on the timing of events associated with spawning, and these studies have proved successful. However, spawning represents only one part of the life history, and therefore, information on eDNA shedding during other life history stages is needed to fill gaps in knowledge. Here, we explored eDNA shedding during early life history (from fertilized eggs until near yolk sac absorption) in Chinook Salmon ( Oncorhynchus tshawytscha ) at three biomasses in a laboratory environment. We found that fertilized eggs shed little eDNA prior to hatching. Hatching coincided with a spike in eDNA, and we observed a significant and positive relationship between eDNA concentration and the number of hatched eggs. The concentration of eDNA shed by larvae after hatching was not consistent across post-hatch sampling days, suggesting developmental and behavioral changes associated with larval ontogeny may affect eDNA shedding rate. These results indicate that eDNA data may be used to identify hatch timing and verify successful reproduction in oviparous aquatic fishes. The application of eDNA to early life history broadens the capacity of eDNA-based methods for assessing population status and trends.

Environmental DNA↗

USGS2021

Survival and growth of suckers in mesocosms at three locations within Upper Klamath Lake, Oregon, 2018

Executive Summary Due to high mortality in the first year or two of life, Lost River ( Deltistes luxatus sp.) and Shortnose suckers ( Chasmistes brevirostris sp.) in Upper Klamath Lake, Oregon rarely reach maturity. In 2015, the U.S. Fish and Wildlife Service began the Sucker Assisted Rearing Program (SARP) to improve early life survival before releasing the fish back into Upper Klamath Lake. Survival and growth rates were compared for fish in mesocosms among three potential release or in-lake rearing sites, and in a pond at the SARP rearing facility. Fish used in this study included a mix of Lost River, Shortnose, and Klamath largescale suckers reared at either U.S. Fish and Wildlife Service or Klamath Tribes fish rearing facilities. These sites were Shoalwater Bay (SWB), Rattlesnake Point (RPT), and Cove Point (CPT). Ninety-nine to 103 suckers tagged with passive integrated transponders (PIT) were placed into each mesocosm for up to 80 days and up to 103 days in the SARP pond. Cessation of movement, as determined by passive detection of tagged fish on remote antennas, indicated mortality. Dissolved-oxygen saturation, temperature, and pH were tracked hourly in each mesocosm. All the suckers placed into the SWB mesocosm died during an extreme hypoxia event. These fish were replaced with another 120 PIT-tagged and 2 untagged hatchery-reared Lost River suckers from the Klamath Tribes Fish Research Facility (KTFRF), of which, all but two died during a second extreme hypoxia event. It was determined that SWB was an unsuitable site for summertime release or rearing of juvenile suckers in 2018. The summer survival rate was ≥86 percent at CPT, RPT, and the SARP pond. Suckers in the SARP pond grew slightly slower and gained less weight relative to increases in length than suckers held at RPT and CPT. All suckers sampled at the start of the study from both the SARP facility and the KTFRF, when water temperatures averaged approximately 18–22 degrees Celsius (°C), were infected with low levels of the gill parasite Ichthyobodo sp. Ichthyobodo sp. was detected on only 1 of 16 suckers sampled from CPT, RPT, and the SARP pond in late September or early October when water temperatures were approximately 16–19 °C, indicating fish were able to shed the parasite in cooler temperatures. Water quality conditions at RPT and CPT were adequate for in-lake rearing of SARP suckers in 2018. Due to interannual differences in water quality conditions, these sites may not be suitable in all years. Future research focused on the suitability of RPT, CPT and other potential sites under in years with varying conditions would be beneficial for improving sucker in-lake rearing practices. Additional research could help to elucidate how size at entry into the mesocosms affects sucker survival.

Oregon↗

USGS2020

Environmental DNA is an effective tool to track recolonizing migratory fish following large‐scale dam removal

Environmental DNA (eDNA) has emerged as a potentially powerful tool for use in conservation and resource management, including for tracking the recolonization dynamics of fish populations. We used eDNA to assess the effectiveness of dam removal to restore fish passage on the Elwha River in Washington State (USA). Using a suite of 11 species‐specific eDNA polymerase chain reaction (PCR) assays, we showed that most targeted anadromous species (five Pacific Salmon species and Pacific Lamprey) were able to pass upstream of both former dam sites. Multiscale occupancy modeling showed that the timing and spatial extent of recolonization differed among species during the four years of post‐dam removal monitoring. More abundant species like Chinook Salmon and Coho Salmon migrated farther into the upper portions of the watershed than less abundant species like Pink Salmon and Chum Salmon. Sampling also allowed assessment of potamodromous fish species. Bull Trout and Rainbow Trout, ubiquitous species in the watershed, were detected at all sampling locations. Environmental DNA from Brook Trout, a non‐native species isolated between the dams prior to dam removal, was detected downstream of Elwha dam but rarely upstream of the Glines Canyon Dam suggested that the species has not expanded its range appreciably in the watershed following dam removal. We found that eDNA was an effective tool to assess the response of fish populations to large‐scale dam removal on the Elwha River.

Environmental DNA↗

USGS2020

Juvenile Lost River and shortnose sucker year-class formation, survival, and growth in Upper Klamath Lake, Oregon, and Clear Lake Reservoir, California—2018 monitoring report

California, Oregon↗

USGS2020

Development of a quantitative PCR assay for detecting Egeria densa in environmental DNA samples

Brazilian elodea ( Egeria densa ) is an invasive freshwater plant that demonstrates widespread ecological impacts in freshwater ecosystems and causes substantial economic damage. Here, we developed an environmental DNA assay for detection of E. densa to provide resource managers with a tool for early detection, identification, and monitoring of invasive populations.

Conservation Genetics Resources↗

USGS2020

Juvenile Lost River and shortnose sucker year-class formation, survival, and growth in Upper Klamath Lake, Oregon and Clear Lake Reservoir, California—2017 Monitoring Report

Executive Summary Populations of federally endangered Lost River ( Deltistes luxatus ) and shortnose suckers ( Chasmistes brevirostris ) in Upper Klamath Lake, Oregon, and Clear Lake Reservoir (hereinafter referred to as Clear Lake; fig. 1), California, are experiencing long-term declines in abundance. Upper Klamath Lake populations are decreasing because juvenile suckers are not surviving and recruiting into the adult population. Most juvenile sucker mortality occurs within the first year of life in Upper Klamath Lake. Annual production of juvenile suckers in Clear Lake appear 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 some 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) better understand when juvenile sucker mortality is greatest; 3) help identify potential causes of high juvenile sucker mortality particularly in Upper Klamath Lake; and 4) monitor for successful juvenile survival in Upper Klamath Lake. The U.S. Geological Survey (USGS) began a summer juvenile sucker monitoring program in 2015 to track cohorts over time in Upper Klamath and Clear Lakes. The juvenile sucker monitoring program involved using trap net data at fixed sites to determine the status of juvenile suckers. Annual variability in apparent age-0 sucker production, juvenile sucker survival, and growth were tracked. Using genetic markers, suckers were classified as one of three taxa; shortnose (combinations of shortnose and Klamath largescale suckers), Lost River, or suckers with genetic markers of both species (Intermediate [Prob]). By using catch data, we generated taxa-specific indices of year-class strength, August–September apparent survival, and overwinter apparent survival. We also examined the prevalence and severity of afflictions such as parasites, wounds, and deformities. The Upper Klamath Lake year-class strength indices for both Lost River and shortnose suckers were slightly lower in 2015 and 2017 than in 2016. The ratios of age-0 Lost River suckers to age-0 shortnose suckers captured in August in Upper Klamath Lake were low in 2015 and 2017, given that adult Lost River suckers are more abundant and more fecund than adult shortnose suckers. This may indicate lower egg, larval, or juvenile survival or poorer spawning success for Lost River suckers than shortnose suckers in these two years. Apparent relative age-0 survival indices for Lost River suckers from August to September in Upper Klamath Lake were greater in 2015 (0.29) than in 2016 (0.16) or 2017 (0.14). Age-0 shortnose sucker catch rates increased between August and September in 2015, possibly indicating new individuals of this species were still recruiting to the lake between the two sampling periods. August to September relative survival indices for Upper Klamath Lake shortnose suckers were 0.35 in 2016 and 0.00 in 2017. We predicted year-class strength would be greater in Clear Lake in years when high spring-time lake elevations and instream flow allowed adult suckers access to spawning habitat in the Willow Creek drainage. Instream flows and lake elevations were sufficient to allow adult suckers to access Willow Creek during the 2016 and 2017 spawning seasons, and age-0 suckers were detected in Clear Lake both years. Higher lake surface elevations and instream flows in 2017 than in 2016 were not associated with higher year-class strength indices in 2017 than in 2016. Low lake surface elevations appeared to limit access by adults to Willow Creek during the 2014 and 2015 spawning seasons and age-0 suckers were not detected in Clear Lake during these years. Nineteen shortnose suckers from the 2014 cohort were captured in Clear Lake in 2017. A 2015 cohort of shortnose suckers was captured as age-1 in 2016 and as age-2 in 2017. The most likely explanation for increasing catch rates of the 2015 cohort is that the higher Willow Creek flows in 2016 and 2017 facilitated the movement of stream-resident suckers, spawned in 2014 and 2015 downstream into Clear Lake. Due to uncertainty in the genetic identification of non-Lost River suckers, these fish are equally likely to be Klamath largescale or shortnose suckers (Hoy and Ostberg, 2015).

California, Oregon↗

USGS2020

A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels

Resource managers may be hesitant to make decisions based on environmental (e)DNA results alone since eDNA is an indirect method of species detection. One way to reduce the uncertainty of eDNA is to identify laboratory‐based protocols that ensure repeatable and reproducible results. We conducted a double‐blind round‐robin analysis of probe‐based assays for DNA of dreissenid ( Dreissena spp.) mussels, which are prolific aquatic invaders that can cause significant economic and ecological impacts. DNA extract from water samples spiked with known amounts of dreissenid DNA and from water samples collected from waters with and without dreissenids were analyzed by four independent research laboratories. We used results to calculate detection repeatability within laboratories and assays, detection reproducibility among laboratories and assays, and estimated dreissenid DNA copy number precision and accuracy. Laboratory and assay repeatability and reproducibility of detection results were high, 91% and 92%, respectively. The estimated copy numbers were neither precise nor accurate for samples spiked with <773 gene copies. These results suggest that eDNA surveillance of dreissenid mussels, using the protocols evaluated herein, can generate reliable detection data for decision‐making. However, managers should be cautious about using the quantitative information often associated with eDNA detections, especially when DNA is at lower abundance. Our results provide strong support that eDNA has the potential to provide repeatable and reproducible evidence under varying laboratory conditions and for different sample water chemistries. This is reassuring since the demand for eDNA surveillance is widespread and number of laboratories that process eDNA samples is growing steadily.

California, Montana, Nevada, New York, Oregon, Was↗