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At least 19 recordsLinked to original sources
USGS2025

Preprint: Simulated seasonal loads of total nitrogen and total phosphorus by major source from watersheds draining to Washington waters of the Salish Sea, 2005 through 2020

The U.S. Geological Survey (USGS) and the Washington State Department of Ecology (Ecology) have developed watershed models of seasonal load estimates of total nitrogen (TN) and total phosphorus (TP) discharging into the Washington waters of the Salish Sea from 2005 through 2020. The modeling approach used was dynamic SPARROW (SPAtially Referenced Regressions On Watershed attributes), a statistical-physical watershed modeling technique, initially applied at large spatial scales to represent long-term average stream loads throughout a stream network, refined here to estimate seasonal TN and TP loads across watersheds to clarify upstream contributions from discernable point and nonpoint sources delivered to marine waters at surface water confluences along the shoreline and quantify when, where, and why they were high or low. Upstream contributing sources included permitted treated wastewater facilities, crop fertilizer, animal feeding operations, septic systems, urban land and stormwater, atmospheric deposition (TN only), nitrogen fixation by Red Alder Alnus rubra trees (TN only), and background geologic material (TP only). Instream load magnitudes and their source compositions varied widely across watersheds, and even within each watershed, yet the largest loads typically occurred in the large rivers during winter and fall when streamflow was highest. Likewise, instream loads were typically lowest in summer during low streamflow, yet the relative instream aquatic decay was highest. The seasonal storage lag component of those nonpoint sources was estimated to contribute a quarter of the seasonal instream load during winter and fall high streamflow and sometimes half of the instream load during summer low streamflow. A key aspect of Ecology’s current Puget Sound Nutrient Source Reduction Project is consideration of upstream watershed contributions of nutrients to their marine-water discharge points. Simulated seasonal loads carried by streams to 63 river mouth marine discharge points 9 ranged by several orders-of-magnitude for both TN and TP due to the spatial and seasonal differences in hydrologic flows, magnitude and timing of contributing sources, and in-stream decay. The Snohomish and Skagit Rivers discharged the largest TN and TP loads, yet the Samish River was shown to have some of the highest TN and TP yields and concentrations. Additionally, a reference scenario was developed to provide an estimate of the pre-industrial local and regional loads.

ESS Open Archive↗
USGS1973

Use of machine-processable field notes in a wilderness mapping project (Granite Fiords area), southeastern Alaska

For reconnaissance geologic mapping and mineral resource evaluation of the Granite Fiords wilderness study area, we developed and used a system of machine-processable field notes. Preprinted field forms standardize notes and serve as checklists that insure collection of all available data. The use of this system cut in half the time required to record data at an outcrop. The system consists of three related but different types of preprinted field sheets, a key to abbreviations and codes, and a set of written instructions. The field sheets include a station sheet for basic outcrop data, a specimen sheet for rock samples, and a geochemical sheet for materials to be chemically analyzed. Data on the field sheets are keypunched on standard IBM cards, then arranged in subfiles and retrieved by using a card sorter. Our system is designed specifically for a region of granitic and metamorphic rocks but is easily modified for use in different geologic terranes. We offer four guidelines for developing a system of machine-processable field notes: (1) Time and money spent to develop the system must be worth its anticipated benefits. (2) The system should be as flexible as possible. (3) It is necessary to tailor the system to a particular geologic terrane or project objective. (4) The system should be as simple and self-explanatory as possible.

Alaska↗
USGS2022

The protectiveness of aquatic life criteria for threatened or endangered aquatic species: Cadmium in California

In the United States, conflicts can arise between the processes to derive aquatic life criteria (ALC) for chemicals under the Clean Water Act (CWA) and the evaluation procedures used in Endangered Species Act (ESA) consultations on the protectiveness of those criteria for protected species. This paper examines the roots of, and possible reconciliation of, one longstanding conflict over cadmium aquatic life criteria in California. This case study includes 1) an overview of occurrences of cadmium in the aquatic environment, 2) factors affecting toxicity of cadmium to aquatic life, 3) a contrast between the analytical procedures of CWA aquatic life criteria derivation and ESA consultation, 4) quantitative estimates of no-effect concentrations of cadmium for 44 ESA listed species in comparison with updated aquatic life criteria, and 5) concludes with suggestions to update California’s aquatic life criteria for cadmium that would be more protective of sensitive ESA listed species. A root cause of conflict is the different levels of biological organization that are the focus of CWA and ESA procedures. The CWA ALC are intended to protect diverse ecosystems by protecting at least 95% of the species richness in communities, allowing that it is acceptable for some species in the residual most sensitive 5% of the community richness to be harmed or even locally extirpated so long as they are not societally important species. The ESA is charged with minimizing harm to individual organisms and disallows increasing risk of extinction or impeding recovery of protected species. With cadmium in California, these procedures converge because some of the most sensitive species to cadmium happen to be surrogates for protected species (acute responses of steelhead/rainbow trout, Oncorhynchus mykiss , and chronic responses of threespine stickleback, Gasterosteus aculeatus ). The present review concludes that while the superseded 1996 cadmium criteria versions would not be fully protective for up to half of the 44 ESA listed aquatic species in California, the updated 2016 versions would be more protective. Still, the review shows that the updated acute criteria would only fully protect the less sensitive half of the distribution of data for steelhead/rainbow trout sensitivity to cadmium, and the chronic criterion still would not protect the listed threespine stickleback. With a data rich species such as rainbow trout, instead of defining acute criteria using a central tendency statistic such as the geometric mean of multiple test responses, using a lower statistic such as the 10th percentile would ensure that the vast majority of a sensitive, protected species (and all less sensitive species) would be protected. Available data for the stickleback indicate it may be highly sensitive to cadmium, but no threshold can be derived from existing data. Additional testing with cadmium and stickleback would be needed to suggest an alternative, quantitative approach.

California↗
USGS2024

A hierarchical model for eDNA fate and transport dynamics accommodating low concentration samples

Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management; however, several factors currently limit the reliability of ecological inference from eDNA sampling. Two particular challenges are 1) determining species source location(s) and 2) accurately and precisely measuring low concentration eDNA samples in the presence of multiple sources of ecological and measurement variability. The recently introduced eDNA Integrating Transport and Hydrology (eDITH) model provides a framework for relating eDNA measurements to source locations in riverine networks, but little empirical work has been done to test and refine model assumptions or accommodate low concentration samples, that can be systematically undermeasured. To better understand eDNA fate and transport dynamics and our ability to reliably quantify low concentration samples, we developed a hierarchical model and used it to evaluate a fate and transport experiment. Our model addresses several low concentration challenges by modeling the number of copies in each PCR replicate as a latent variable with a count distribution and conditioning detection and quantification on replicate copy number. We provide evidence that the eDNA removal rate declined through time, estimating that over 80% of eDNA was removed over the first 10 meters, traversed in 41 seconds. After this initial period of rapid decay, eDNA decayed slowly with consistent detection through our farthest site 1km from the release location, traversed in 250 seconds. Our model further allowed us to detect extra-Poisson variation in the allocation of copies to replicates. We extended our hierarchical model to accommodate a continuous effect of inhibitors and used our model to provide evidence for the inhibitor hypothesis and explore the potential implications. While our model is not a panacea for all challenges faced when quantifying low-concentration eDNA samples, it provides a framework for a more complete accounting of uncertainty.

BioRxiv↗
USGS2024

Assessing the sustainability of Pacific walrus harvest in a changing environment

Harvest sustainability is a primary goal of wildlife management and conservation, and in a changing world it is increasingly important to consider environmental drivers of population dynamics alongside harvest in cohesive management plans. This is particularly pertinent for harvested species that are acutely experiencing effects of climate change. The Pacific walrus ( Odobenus rosmarus divergens ), a critical traditional subsistence resource for indigenous communities, is simultaneously subject to rapid habitat loss associated with diminishing sea ice and an increasing anthropogenic footprint in the Arctic. We developed a theta-logistic population modeling-management framework to evaluate various harvest scenarios combined with four potential climate/disturbance scenarios (ranging from optimistic–pessimistic) which simulates Pacific walrus population dynamics to the end of the 21 st century. We considered two types of harvest strategies: (1) adaptive harvest scenarios wherein harvest is calculated as a percentage of the population and annual harvests are updated at set intervals as the population is reassessed, and (2) non-adaptive harvest scenarios wherein annual harvest remains constant. All climate/disturbance scenarios indicated declines of varying severity in Pacific walrus abundance to the end of the 21 st century, even in the absence of harvest. However, we found that an adaptive annual harvest of 1.23% of the independent-aged female subset of the population (e.g., 1,280 independent-aged females harvested in 2020, representing contemporary harvest levels) met our criterion for sustainability (>70% probability of maintaining population abundance above maximum net productivity level) under all climate/disturbance scenarios, accepting a medium risk tolerance level of 25%. This suggests that the present rate of Pacific walrus harvest is sustainable and will continue to be—provided the harvest adapts to match changes in population dynamics. Our simulations suggest that a sustainable non-adaptive harvest is also possible, but only at low levels if the population declines as expected. Applying a constant annual harvest of 1,280 independent-aged females (equivalent to contemporary harvest levels of 1.23) exceeded our criterion for sustainability and resulted in a >5% chance of quasi-extinction by the end of the 21 st century under three of the four climate/disturbance scenarios we evaluated. Our results highlight the importance of adaptive co-management strategies, and we suggest such modeling frameworks are useful for managing for harvest sustainability in a changing climate.

BioRxiv↗
USGS2024

Estimating species-specific U.S. waterfowl harvest

The U.S. Fish and Wildlife Service monitors species-specific waterfowl (ducks, seaducks, geese, and brant) harvest through two hunter surveys, one that estimates the total harvest for each waterfowl group, and a second that estimates the species composition of each waterfowl group. Point estimates for species-specific harvest can be computed by multiplying the estimated total harvest by the estimated proportion of the total harvest of each species. However, to date, no uncertainty estimates have been available. Here, we combine these two data sources to provide species-specific harvest estimates at the state and flyway level while characterizing the uncertainty via Bayesian estimation. We take a similar approach to Smith et al . (2022) , providing both estimates that treat yearly data as independent and estimates that share information across years via a random walk process. We then discuss the advantages and disadvantages of each approach.

BioRxiv↗
USGS2024

Mapping eelgrass cover and biomass at Izembek Lagoon, Alaska, using in-situ field data and Sentinel-2 satellite imagery

Two eelgrass ( Zostera marina ) maps of Izembek Lagoon, Alaska, were generated by first creating maps of spectrally unique classes from each of two Sentinel-2 satellite images collected on July 1, 2016, and August 14, 2020, then attributing the spectral classes with information about eelgrass conditions based on field data. Maps depicting various eelgrass metrics, such as percent cover and modeled biomass, were generated using summaries of the ground data that spatially intersected each spectral class. Comparisons between the 2016 and 2020 Sentinel-2 maps of eelgrass distributional extent, as well as a 2006 Landsat map, indicated that areas where eelgrass presence may have declined between 2006 and 2020 were most prevalent in the central part Izembek Lagoon, while areas of possible biomass decline were more prevalent in the southern part between 2016 and 2020. Monitoring eelgrass conditions at Izembek Lagoon with satellite imagery and concurrent ground data provides capabilities for making comparisons over time, but the influences of tide levels, growing season phenology, and spatiotemporal co-registration accuracy should be considered when designing and interpreting change detection analyses.

Alaska↗
USGS2024

Evidence for recruitment-mediated decline in an Eastern box turtle (Terrapene carolina carolina) population based on a 30-year capture-recapture data set from Maryland

The Eastern box turtle ( Terrapene carolina carolina ) population at the Jug Bay Wetlands Sanctuary, Lothian, MD has been monitored continuously for 29 years (1995-2023). We used open population capture-recapture models (Jolly-Seber) to estimate annual population size, survival probability, and recruitment rate. The model allows for unknown sex of individuals and includes information on individuals found dead. Our analysis documents a long-term decline of approximately 67% in box turtle population size at the Sanctuary over this nearly three-decade period. We estimate annual survival for both males and females, which does not show a systematic increase or decrease over time, averaging about 0.90 (95% CI: 0.86, 0.93) for females and 0.97 (95% CI: 0.94, 0.98) for males. Conversely, per-capita recruitment shows a marked decline over the first 15 years of the record, suggesting that population declines may be due to reduced recruitment. Conservation efforts for the species could benefit from a formal population viability analysis to understand the relative effects of survival and recruitment on changes in population size for this long-lived species.

BioRxiv↗
USGS2024

Ungulate personality and the human shield contribute to long-distance migration loss

Long-distance ungulate migrations are declining and past research has focused on preserving migration paths where habitat fragmentation and loss disrupts movement corridors. However, changing residency-migration tradeoffs are the stronger driver of long-distance migration loss in some populations. The human shield effect relative to predation risk and anthropogenic food resources likely shapes these tradeoffs, but individual animals also vary in their propensity to tolerate proximity to humans and developed areas. We investigated how personality relative to human-habituation affects migration behavior. We categorized elk as bold or shy based on use of anthropogenic food resources identified through a clustering algorithm applied to GPS collar data. Bold elk were 4 times more likely to select wintering areas close to human activity and migrated 60% shorter distances compared to shy elk. As a result, elk wintering grounds were spatially structured such that conflict- and disease-prone individuals selected areas adjacent to human activity. Our results suggest that bold personality traits act as a precursor to human-habituation, which permits bold elk to reap the forage and predation rewards that occur in suburban landscapes. A multi-pronged approach beyond just maintaining habitat corridors may be necessary to conserve long-distance migrations for species that can become human-habituated.

BioRxiv↗
USGS2024

Rare habitats, rare species, and invasive predators highlight management complexities in the Colorado River system

Long-term drought caused Lake Powell, a reservoir on the Colorado River (USA), to decline to its lowest elevation in >50 years during 2022–2023, allowing warm water to pass through intakes of Glen Canyon Dam and facilitating invasion by non-native Smallmouth Bass ( Micropterus dolomieu ). Establishment of bass downstream of the dam could threaten persistence of several native fishes, including two federally listed species. Subsequent detection of larval Smallmouth Bass in a spring-fed slough (river mile -12 slough) connected to the river in Glen Canyon National Recreation Area (NRA) increased urgency to stem further invasion. The National Park Service is evaluating proposed actions to limit effects from non-native predators on native species in the Colorado River, including potentially channelizing the slough. This locally rare, spring-fed waterbody provides habitat for other species, including Western Tiger Salamanders ( Ambystoma mavortium subsp.) of uncertain origin. We found salamanders from the slough had two distinct mitochondrial DNA haplotypes identical to sequences from nearby Arizona Tiger Salamander ( A. m. nebulosum ) populations, confirming they are the native genotype. We detected Red-spotted Toads ( Anaxyrus punctatus ) and Woodhouse’s Toads ( A. woodhousii ) from three other sites in Glen Canyon NRA and 34 sites in adjacent, downstream Grand Canyon National Park (spanning ∼464 km of river) with environmental DNA and traditional surveys. However, we did not detect salamanders elsewhere, matching prior information that salamanders are rare in the Colorado River corridor below Glen Canyon Dam. Based on this information, we discuss management options for the local population of Arizona Tiger Salamanders.

BioRxiv↗
USGS2025

Evaluation of a rapid assessment function to aid monitoring and management of common ravens (Corvus corax) in Washington state

Expanding human enterprise leading to resource subsidies for generalist species has resulted in widespread increases in common raven ( Corvus corax ) populations across the Western U.S. Ravens are an efficient predator and increased population abundance has led to adverse effects to multiple sensitive prey species. In regions where problematic interactions between ravens and their prey exist, managers seek efficient and effective tools for monitoring and controlling expanding raven populations. We previously developed a Rapid Assessment Function (RAF) for managers to quickly estimate raven population density and assess the need for management actions. We developed the RAF for the Great Basin (GB RAF) by first estimating raven density using robust distance sampling protocols with >30,000 raven point count surveys from sagebrush ecosystems in California, Nevada, Idaho, and Oregon across 131 field sites and years. We then used the relationship between raven density estimates from distance sampling and n ravens observed site-year / n surveys site-year (that is, raven index) at each site-year combination to develop a function that accounts for detection probability and adjusts simple counts to provide a prediction of ‘true’ density. Our function produced reliable density estimates given approximately 50–100 surveys, thereby reducing the field-based and analytical efforts typically needed to estimate raven density, facilitating more efficient raven management in open sagebrush habitats. In this study, we sought to test our original GB RAF using data from sagebrush ecosystems outside of the Great Basin. Using raven point count data from two field site units in Washington state collected from 2016 to 2023, we calculated density estimates from distance sampling methods, comparable to what was done for previous analyses. We then used the GB RAF to generate predictions of density and compared those values to the more robust estimates from distance sampling. Additionally, we developed modified RAFs specifically for Washington data (WA RAFs) to assess how well they predicted raven density compared to the GB RAF. We found the detection curves estimated for the Washington sites largely aligned with those used to generate the original GB RAF. Furthermore, the estimates from the GB RAF exhibited similar or higher correlation with densities calculated from distance models ( Pearson’s r = 0.73) than the modified WA RAFs with 1.33 km and 1.25 km truncation distances ( Pearson’s r = 0.63 and 0.73, respectively). Producing an equivalently performing modified WA RAF would likely necessitate more data to reduce estimation error and produce more reliable estimates. These results provide evidence for the applicability of our GB RAF for more widespread use within sagebrush ecosystems, possibly negating the need for locally developed RAFs. Continued assessments of the GB RAF outside of the Great Basin would further verify its applicability across the sagebrush biome.

BioRxiv↗
USGS2025

Piping Plover home ranges do not appear to be impacted by restoration of barrier islands and headlands

Restoration of barrier island and headland habitats can alter existing and create new habitats, which may impact wildlife occupying these areas such as the threatened Piping Plover ( Charadrius melodus ). We used resight data from banded birds to develop minimum convex polygon (MCP) and kernel density estimates (KDE) of individual Piping Plover home ranges to investigate whether changes in habitat use resulted from restoration activities at Whiskey Island and Caminada Headland, Louisiana. We quantified home range areas for each season and compared changes among pre-restoration, active restoration, and post-restoration phases at each site. We had sufficient sample sizes from Whiskey Island to compare home ranges derived by MCP during the pre-restoration phase to the active restoration phase. However, we did not have enough resight data to analyze post-restoration phase by MCP or any phase by KDE at Whiskey Island. For Caminada Headland, we were able to compare all phases of restoration using MCP, but only had sufficient data to compare pre-restoration and active restoration phases using KDE. Aside from one significant decrease in core (50% isopleth) home range at Caminada Headland when comparing MCPs between post-restoration (∼8 ha) and pre-restoration (∼11 ha) phases, we found no other differences in home range size across phases at either of our study sites. The sum of all evidence generally indicating no change to Piping Plover home range size suggests that barrier island and headland restoration did not have significant positive or negative impacts. The weak response to restoration activities further suggests that birds are using similar or smaller amounts of habitat after restoration is complete and may not need to expand their foraging range following restoration. Further study can help to understand how species of conservation concern respond to coastal restoration efforts, which is critical for establishing comprehensive conservation strategies aimed at species recovery.

BioRxiv↗
USGS2025

Sentinel-2 based estimates of rangeland fractional cover and canopy gap class for the western United States

Rangelands are extensive ecosystems, providing important ecosystem services while undergoing continuous change. As a result, improved monitoring technologies can help better characterize vegetation change. Satellite remote sensing has proven effective in this regard, tracking vegetation dynamics at broad and fine scales. We leveraged the spatial, spectral, and temporal resolution of Sentinel-2 satellites to estimate fractional cover and canopy gap across rangelands of the western United States. We produced annual, 10 m spatial resolution estimates of fractional cover and canopy gap size class for years 2018 to 2024. Fractional cover estimates include that of common plant functional types (annual forb and grass, bareground, littler, perennial forb and grass, shrub, tree) and select genera (including invasive annual grass species, pinyon-juniper species, and sagebrush species); canopy gap size classes include gap sizes 25 to 50, 51 to 100, 101 to 200, and greater than 200 cm. We make these data available as Cloud Optimized GeoTIFFs, organized as 75×75 km tiles covering the 17 western states of the United States.

BioRxiv↗
USGS2025

Scalable environmental DNA methods reveal strong associations between landscape-scale forest habitat and insect richness

While aquatic environmental DNA (eDNA) methods have reached relative maturity, terrestrial eDNA methods are nascent and have yet to reach widespread use. Field-ready applications require eDNA survey methods where samples are easy to collect by inexperienced practitioners, easy to transport between the field and lab, and easy to process thereafter. Here, we demonstrate methods that satisfy these requirements and show strong potential for characterizing diverse terrestrial eDNA samples collected from flower and leaf surfaces. We used novel methods to collect and process 236 flower eDNA samples and 21 leaf surface eDNA samples, obtaining 2,228 Arthropoda eDNA detections spanning 175 families using amplicon sequencing of two genetic markers. Detected taxa were diverse and included numerous groups of conservation concern, such as bees (Hymenoptera; Anthophila, 32 genera spanning 5 families) and Lepidoptera (209 genera from 21 families). Data reveal strong associations between insect community richness and remotely sensed measures of forest habitat, providing a quantitative perspective of relevance to insect conservation. It is increasingly clear that a variety of organisms readily disperse eDNA throughout the environment, supporting the notion that eDNA will be a powerful tool for characterizing species distributions and monitoring at-risk species. However, we conclude that researchers seeking to characterize fine-scale habitat associations or plant-pollinator interactions using eDNA will need to carefully design studies with appropriate field controls, such as the leaf surface eDNA samples collected here.

BioRxiv↗
USGS2025

Failure to meet the exchangeability assumption in Bayesian multispecies occupancy models: Implications for study design

Bayesian hierarchical models are ubiquitous in ecology. Random effect model structures are often employed that treat individual effects as deviations from larger population-level effects. In this way individuals are assumed to be "exchangeable" samples. Ecologists may address this exchangeability assumption intuitively, but might in certain modeling contexts ignore it altogether, including in situations where it may have large implications for study design. Multispecies occupancy models based on detection/non-detection data are an approach that can be utilized by those tasked with monitoring rare and endangered species because most literature suggests that, compared to single species occupancy models, improved parameter estimates are assured. Yet, we illustrate through a power analysis how sampling requirements to detect experimental treatment effects vary tremendously depending on whether the species exchangeability assumption is met. The degree to which species in a community respond similarly to covariates governs the ability to accurately estimate parameters using multispecies occupancy models. Detecting small or moderate changes in occupancy resulting from habitat restoration treatments may be impossible for small datasets (e.g., < 36 sampling locations, each surveyed < 8 times) even with a paired treatment-control design if the exchangeability assumption is violated. By contrast, when the assumption is met, small effects may be confidently estimated with as few as 12 sampling locations (6 pairs) and 6-8 survey events. Often, it may be impossible to know whether the exchangeability assumption is met. The statistical power needed to accurately estimate species-specific effects using detection/non-detection multispecies occupancy models depends on the unknown values of treatment effects and whether responses by species in the community diverge. When the species exchangeability assumption is violated, and at lower levels of sampling effort, multispecies occupancy models may provide worse inference than single species occupancy models.

BioRxiv↗
USGS2025

Development of a two-stage life cycle model to inform the Trap and Haul Program for Coho salmon in the Lewis River, Washington

Restoration of salmon populations in the upper Lewis River Basin depends on a trap-and-haul program owing to the Lewis River Hydroelectric Project (Project) operated by PacifiCorp and Cowlitz PUD (Utilities), which has been a barrier to salmon passage since the 1930s. Thus, sustaining the Coho salmon ( Oncorhynchus kisutch ) population upstream of the Project currently depends on two fundamental factors: (1) the collection of upstream migrating adult Coho salmon at Merwin Dam, the lower most dam within the Project, and transporting them by truck to spawn above Swift Dam, the upper most dam within the Project; and (2) the collection of out-migrating juvenile Coho salmon at the downstream collection facility at Swift Dam for transport and release below the Project. The reintroduction program began once the downstream collection facility at Swift Dam was commissioned in late-2012 with the first year of transport data being collected in 2013. Over the past decade, the Utilities have been collecting data on juvenile outmigrants and adult fish returns at the dams. The need to construct a life cycle model for Lewis River anadromous fish was identified by the Lewis River Aquatic Technical Subgroup, with the understanding that many years (>15) of data collection are needed to adequately measure the life cycle production of coho salmon. Use of past data to construct models could help inform future data collection and provide a framework that can be updated annually to measure trap and haul program performance within a life cycle context (Note: Data are not currently available from PacifiCorp. Contact organization Chris Karchesky for further information). Because Coho salmon can live as long as five years, estimating demographic parameters for Coho salmon populations over their life cycle requires at least 10 or more years of data collection. Over the past decade, PacifiCorp has been collecting data on fish collection efficiency and the numbers of adult and juvenile salmon transported around the Lewis River dams, providing sufficient data to formulate a life cycle model that can guide future data collection efforts and provide preliminary information to resource managers The goal of the statistical life cycle model was to estimate annual production and survival during two critical life-stage transitions (1) the freshwater production from escapement of adults released upstream of Swift Dam, and the collection of downstream migrating juveniles at the passage facility at Swift Dam, and (2) the smolt-to-adult survival from the time of collection at Swift Dam to their return as adults. We used the Beverton-Holt stock-recruitment model to estimate juvenile production from the number of spawners. This approach allowed us to test for density dependence at current spawner abundances while estimating annual productivity, defined as the number of juveniles produced per spawner at low spawner abundance. Productivity was then expressed as a function of the number of juveniles collected and transported downstream of the Project. Because juvenile Fish Collection Efficiency (FCE) directly affects the number of juveniles that survive to continue downstream migration, FCE is a primary determinant of fish production. Consequently, the modeling framework is well suited to evaluate the performance of trap and haul programs within a life cycle context. The objectives of this study were to: (1) gather and collate available data on adult and juvenile Coho salmon at Merwin and Swift dams, (2) quantify adult escapement, juvenile abundance, and the age at outmigration and adult return, (3) describe, formulate, and fit the integrated population model (IPM) to the data, and (4) summarize our findings, identify data gaps, and identify potential opportunities for future studies that could provide information used to improve model estimation and inference. Our key findings were: (1) over and above the number of spawning females, FCE was the primary factor affecting productivity of Coho salmon above Swift Dam, (2) smolt-to-adult return (SAR) rates were relatively high considering that harvest was included in the estimate, averaging about 4.5% and ranging as high as 12.9%, and (3) juvenile capacity upriver of Swift Dam was difficult to estimate due to the limited range in spawning females over the time series of data, suggesting the model may be improved by collecting data at higher spawner abundances. In addition, by including FCE in the model, we estimated that the median pre-collection productivity, defined as the number of juveniles produced per spawner when FCE = 1, was 64 juveniles per spawner. Because this two-stage life cycle model partitions factors that affect fish production in river versus the ocean, the model estimates should help inform fishery managers about the overall role that fish collection at Swift Dam plays in the recovery and sustainability of Lewis River Coho salmon. By providing the model with (1) more years of data, (2) higher numbers of spawning females, and (3) data on age at juvenile migration in relation to age at adult return greater certainty in the estimates of capacity and SAR can be attained. Ultimately, information provided by the model can assist in the evaluation and continued improvement of the current trap and haul program to support anadromous fishes in the Lewis River Basin.

BioRxiv↗
USGS2025

Sensitive environmental DNA methods for low-risk surveillance of at-risk bumble bees

Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection densities on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterization of whole bumble bee communities, including rare and critically endangered species such as the rusty pathed bumble bee (RPBB; Bombus affinis ). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Relative to flower eDNA samples, sequenced field negative controls resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the method is cost-effective and highly scalable for semi-quantitative characterization of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.

BioRxiv↗
USGS2025

Novel adomaviruses associated with blotchy bass syndrome in black basses (Micropterus spp.)

Black bass ( Micropterus spp. ) are the most important warmwater game fishes in the United States. They have high socioeconomic and recreational value and support an important aquaculture industry. Since 2008, fisheries managers have been reporting the observation of hyperpigmented melanistic lesions (HPMLs) on smallmouth bass ( M. dolomieu ) in different ecoregions of the United States. Similar HPMLs have been observed in largemouth bass ( M. nigricans ) since the 1980’s. Here, we report a close association between novel adomaviruses and the hallmark blotchy clinical presentation of hyperpigmented lesions on the skin smallmouth and largemouth black bass and provide evidence that satisfies Rivers’ postulates. The two adomaviruses are structurally and phylogenetically similar but share only 68.0% identity at aligned nucleotide sites and each has been found in only one host species to date. The manifestation of this skin disease appears to be seasonal in both species, primarily affects adults and is of unknown health consequence. Although the significance of infection to fish health remains unclear, understanding the disease ecology of these can inform biosecurity and the interjurisdictional movement of individuals. Moreover, as hyperpigmentation in other fish species is often idiopathic, our findings reframe perspectives for future investigations into this clinical presentation in other species.

BioRxiv↗