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USGS2021

Estimating detection and occupancy coefficients for the Pacific Islands coral reef fish species

The data-limited stock assessment models used to monitor the status of coral reef fish species in the Western Pacific region are dependent upon accurate estimates of standing stock biomass generated from underwater visual surveys of reefs. However, the imperfect detection of and variable occupancy of habitat by reef fishes are not currently accounted for in these estimates. Therefore, the objective of this project was to estimate detection and occupancy coefficients for the species listed in the Western Pacific Regional Fishery Management Council’s Fishery Ecosystem Plans by analyzing the Pacific Island Fishery Science Center-Coral Reef Ecosystem Program Reef Fish Dataset. These detection and occupancy coefficients would then be applied to refine standing stock biomass estimates. In general, species with higher detection probabilities and/or lower occupancy rates tended to exhibit the greatest differences in the estimates of standing stock biomass calculated with and without accounting for detection and occupancy. The standing stock biomass of most reef fish species seem to be underestimated when detection and occupancy are not accounted for. However, the standing stock biomass of larger-bodied targeted species, such as jacks, snappers, and groupers, seem to be over-estimated relative to the estimates generated when accounting for occupancy and detection. While there are still issues to resolve regarding how well the current data collection methods meet the underlying assumptions of the detection and occupancy modeling approach, the inclusion of detection and occupancy coefficients seems likely to improve estimates of standing stock biomass of coral reef fish species.

Hawaii↗

USGS2017

Isolation and characterization of the fall Chinook aquareovirus

Background Salmon are paramount to the economy, ecology, and history of the Pacific Northwest. Viruses constitute one of the major threats to salmon health and well-being, with more than twenty known virus species that infect salmon. Here, we describe the isolation and characterization of the fall Chinook aquareovirus, a divergent member of the species Aquareovirus B within the family Reoviridae . Methods The virus was first found in 2014 as part of a routine adult broodstock screening program in which kidney and spleen tissue samples from healthy-appearing, adult fall Chinook salmon ( Oncorhynchus tshawytscha ) returning to a hatchery in Washington State produced cytopathic effects when inoculated onto a Chinook salmon embryo cell line (CHSE-214). The virus was not able to be confirmed by an RT-PCR assay using existing aquareovirus pan-species primers, and instead was identified by metagenomic next-generation sequencing. Metagenomic next-generation sequencing was used to recover the full genome and completed using 3′ RACE. Results The genome of the fall Chinook aquareovirus contains 11 segments of double-stranded RNA totaling 23.3 kb, with each segment flanked by the canonical sequence termini found in the aquareoviruses. Sequence comparisons and a phylogenetic analysis revealed a nucleotide identity of 63.2% in the VP7 gene with the Green River Chinook virus, placing the new isolate in the species Aquareovirus B . A qRT-PCR assay was developed targeting the VP2, which showed rapid growth of the isolate during the initial 5 days in culture using CHSE-214 cells. Conclusions This sequence represents the first complete genome of an Aquareovirus B species. Future studies will be required to understand the potential pathogenicity and epidemiology of the fall Chinook aquareovirus.

Virology Journal↗

USGS2025

Wave driven cross shore and alongshore transport reveal more extreme projections of shoreline change in island environments

Coastal erosion, intensified by sea level rise, poses significant threats to coastal communities in Hawaiʻi and similar island communities. This study projects long-term shoreline change on the Hawaiian Island of O‘ahu using the data-assimilated CoSMoS-COAST shoreline change model. CoSMoS-COAST models four key shoreline processes: (1) Alongshore transport, (2) Recession due to sea level rise, (3) Cross-shore transport due to waves, and (4) Residual processes represented by a linear trend term. This study marks the first application of CoSMoS-COAST for an oceanic equatorial island with narrow beaches and a dynamic wave climate. The model is informed with a novel combination of shoreline data derived from high-resolution imagery from Planet, Sentinel-2, and Landsat satellites, wave-climate hindcasts specific to Hawai‘i, and regional beach-slope surveys. On a dynamic northern Oʻahu beach, the model achieved a root mean square error of 9.4 m between observations and model output. CoSMoS-COAST predicts that 81% of O‘ahu’s sandy beach coastline could experience beach loss by 2100; with 39.8% of this loss happening by 2030. This represents an increase, 43.3%, in net landward shoreline change compared to previous erosion forecasts, for 0.3 m of sea level rise (2050). Additionally, dynamic processes such as cross-shore equilibrium processes and alongshore sediment transport, play a large contribution to gross shoreline change within the next decade, particularly on O ‘ahu’s north and west shores. In the long term, we find that recession due to sea level rise and residual processes dominate, but dynamic, wave-driven processes (longshore and cross-shore transport) still account for 34% of shoreline change between present and 2100. We assert dynamic, wave-driven processes are a crucial addition for accurate modeling of island sandy beach environments. These findings have implications for O‘ahu’s coastal planning and development, suggesting updates to shoreline policies that rely upon erosion forecasting, and highlights the importance of incorporating wave and alongshore transport in erosion models for other Pacific islands.

Hawaii↗

USGS2014

The 1946 Unimak Tsunami Earthquake Area: revised tectonic structure in reprocessed seismic images and a suspect near field tsunami source

In 1946 at Unimak Pass, Alaska, a tsunami destroyed the lighthouse at Scotch Cap, Unimak Island, took 159 lives on the Hawaiian Islands, damaged island coastal facilities across the south Pacific, and destroyed a hut in Antarctica. The tsunami magnitude of 9.3 is comparable to the magnitude 9.1 tsunami that devastated the Tohoku coast of Japan in 2011. Both causative earthquake epicenters occurred in shallow reaches of the subduction zone. Contractile tectonism along the Alaska margin presumably generated the far-field tsunami by producing a seafloor elevation change. However, the Scotch Cap lighthouse was destroyed by a near-field tsunami that was probably generated by a coeval large undersea landslide, yet bathymetric surveys showed no fresh large landslide scar. We investigated this problem by reprocessing five seismic lines, presented here as high-resolution graphic images, both uninterpreted and interpreted, and available for the reader to download. In addition, the processed seismic data for each line are available for download as seismic industry-standard SEG-Y files. One line, processed through prestack depth migration, crosses a 10 × 15 kilometer and 800-meter-high hill presumed previously to be basement, but that instead is composed of stratified rock superimposed on the slope sediment. This image and multibeam bathymetry illustrate a slide block that could have sourced the 1946 near-field tsunami because it is positioned within a distance determined by the time between earthquake shaking and the tsunami arrival at Scotch Cap and is consistent with the local extent of high runup of 42 meters along the adjacent Alaskan coast. The Unimak/Scotch Cap margin is structurally similar to the 2011 Tohoku tsunamigenic margin where a large landslide at the trench, coeval with the Tohoku earthquake, has been documented. Further study can improve our understanding of tsunami sources along Alaska’s erosional margins.

Alaska↗

USGS2023

Juvenile salmonid monitoring to assess natural recolonization following removal of Condit Dam on the White Salmon River, Washington, 2016–21

Condit Dam was removed from river kilometer (rkm) 5.3 of the White Salmon River, Washington, in 2011 and 2012 after blocking upstream passage of anadromous fish for nearly 100 years. The dam removal opened habitat upstream and improved habitat downstream with addition of cobble and gravel to a reach depauperate of spawning and rearing habitat. We assessed juvenile anadromous salmonid abundance and distribution in the subbasin from 2016 through 2021 to evaluate the efficacy of natural recolonization. We sampled for outmigrant smolts and other life-history stages at a rotary screw trap at rkm 2.3 and for juvenile abundance at sites in Buck and Rattlesnake Creeks, two primary tributaries upstream from the former dam location. We estimated smolt abundance of steelhead ( Oncorhynchus mykiss ) and coho salmon ( O. kisutch ) at the screw-trap site during most years of the study. High flow and missed trapping days in 2017 precluded estimates, and the trap was not fished during 2020 because of the onset of the COVID-19 pandemic. Steelhead smolt-abundance estimates ranged from 3,581 to 5,851 fish; coho salmon smolt-abundance estimates ranged from 1,093 to 1,773 fish, although in 2021, only 2 coho salmon smolt were captured and no estimate was made. Other species and life stages also were captured in the screw trap. Steelhead and coho salmon fry and parr, and Chinook salmon ( O. tshawytscha ) fry were captured, indicating the presence and likely use of improved habitat downstream from the former dam site by multiple life stages and spawning success upstream from the screw-trap site. Chinook salmon fry were captured, indicating spawning success upstream from the screw-trap site. Fry numbers varied greatly by day and year. Yearly variation in Chinook and coho salmon fry numbers may have been influenced by high flows following spawning causing redd scour and egg-to-fry mortality. Three bull trout ( Salvelinus confluentus ) were caught in the screw trap, one in June 2018, one in June 2019, and one in June 2021. All three bull trout showed smolt characteristics and were tagged with passive integrated transponders (PITs). The bull trout captured in June 2018 was detected at Bonneville Dam Corner Collector several days later, indicating likely anadromy. We also captured lamprey in the screw trap: 44 during 2018, 31 during 2019, and 11 during 2021; we believe most were adult brook lamprey ( Lampetra richardsoni ), although some could have been Pacific lamprey ( Entosphenus tridentatus ) macropthalmia. We confirmed the presence of juvenile steelhead (through smolt origin data) and coho salmon in Mill, Buck, and Rattlesnake Creeks, which are all upstream from the former site of Condit Dam. Juvenile salmonid abundance sampling at a site in Buck Creek during 2016–20 indicated the presence of juvenile coho salmon in all years except 2020. Total salmonid abundance (steelhead and coho salmon combined) at the Buck Creek site each year exceeded abundance in sampling prior to dam removal in 2009 and 2010. Juvenile salmonid abundance sampling in Rattlesnake Creek during 2016–20 indicated the presence of juvenile coho salmon in 2017, 2018, and 2019. Total juvenile salmonid abundance at the Rattlesnake Creek site was highly variable, sometimes exceeding and sometimes less than abundance prior to dam removal during 2001–05. During the period covered by this report, adult salmonid returns to the Columbia River were decreasing, largely because of marine survival. The extent to which this basin-wide decrease affected adult returns and juvenile populations in the White Salmon River subbasin is not known. Despite a period of poor marine survival, PIT-tagged smolt and juvenile steelhead and coho salmon from the screw trap and tributaries returned to Bonneville Dam. Smolt-to-adult return rates from the screw trap to Bonneville Dam were similar to those in other nearby rivers during this period. However, data are still incomplete for some years and sample sizes were low. Future tagging and monitoring would be beneficial to track this valuable metric. Genetic samples from steelhead smolt and parr collected at the screw trap and some main-stem electrofishing during 2016 were analyzed for Genetic Stock Identification (GSI) by CRITFC. Preliminary data showed that White Salmon River fish were the most common at about 42 percent, with 19 percent typing to Hood River, Oregon stock, and about 26 percent typing to Skamania stock, a common hatchery stock in the area. Winter and summer runs were represented in the samples. Juvenile salmonid sampling in the White Salmon River, Washington, following removal of Condit Dam, demonstrated that anadromous salmonids are using newly opened habitat upstream from the former dam site and improved lower river habitat. Steelhead and coho salmon smolts are being produced upstream from the former dam site, and some have returned to Bonneville Dam as adults. Chinook salmon spawning upstream from our smolt trap site are producing fry. These results are encouraging for success of the strictly natural recolonization strategy. However, declines in anadromous runs to the larger Columbia River Basin also likely have affected the White Salmon runs and our data may not reflect full capacity of the White Salmon River subbasin juvenile production. Continued abundance, distribution, and GSI monitoring will help to track the evolution of anadromous fish in the White Salmon River under a natural recolonization strategy.

Washington↗

USGS2001

Constraining controls on carbonate sequences with high-resolution chronostratigraphy: Upper Miocene, Cabo de Gata region, SE Spain

A high-resolution chronostratigraphy has been developed for Miocene shallow-water carbonate strata in the Cabo de Gata region of SE Spain for evaluation of local, regional and global factors that controlled platform architecture prior to and during the Messinian salinity crisis. Paleomagnetic data were collected from strata at three localities. Mean natural remanent magnetization (NRM) ranges between 1.53 ?? 10-8 and 5.2 ?? 10-3 Am2/kg. Incremental thermal and alternating field demagnetization isolated the characteristic remanent magnetization (ChRM). Rock magnetic studies show that the dominant magnetic mineral is magnetite, but mixtures of magnetite and hematite occur. A composite chronostratigraphy was derived from five stratigraphic sections. Regional stratigraphic data, biostratigraphic data, and an 40Ar/39Ar date of 8.5 ?? 0.1 Ma, for an interbedded volcanic flow, place the strata in geomagnetic polarity Chrons C4r to C3r. Sequence-stratigraphic and diagenetic evidence indicate a major unconformity at the base of depositional sequence (DS)3 that contains a prograding reef complex, suggesting that approximately 250 000 yr of record (Subchrons C3Br.2r to 3Br.1r) are missing near the Messinian-Tortonian boundary. Correlation to the GPTS shows that the studied strata represent five third- to fourth-order DSs. Basal units are temperate to subtropical ramps (DS1A, DS1B, DS2); these are overlain by subtropical to tropical reefal platforms (DS3), which are capped by subtropical to tropical cyclic carbonates (Terminal Carbonate Complex, TCC). Correlation of the Cabo de Gata record to the Melilla area of Morocco, and the Sorbas basin of Spain indicate that early - Late Tortonian ramp strata from these areas are partially time-equivalent. Similar strata are extensively developed in the Western Mediterranean and likely were influenced by a cool climate or influx of nutrients during an overall rise in global sea-level. After ramp deposition, a sequence boundary (SB3) in Cabo de Gata correlates with a sequence boundary in Morocco and a published third-order eustatic fall suggesting at least a partial eustatic control for the sequence boundary. Coral reefs began to develop earlier in Cabo de Gata than at Melilla or Sorbas, arguing for local factors affecting this major environmental transition. Later Messinian reefs (DS3) from all areas are time-equivalent, suggesting a regional or global control on their formation. Some Halimeda-rich horizons in the Western Mediterranean are not time-equivalent event strata as hypothesized by others. Correlation of the relative sea-level curve for the fringing reef complex (DS3) with a published eustatic curve suggests at least a partial third-order global eustatic control for the highstand part of the sequence. Downstepping DS3 reefs and initial subaerial exposure of earlier DS3 reef strata approximately correlate with initiation of a series of subaerial unconformities in the South Pacific. The longer-term relative fall in sea-level during DS3 downstepping reef progradation does not correlate with a published third-order eustatic fall. Eustatic sea-level fluctuations may have been associated with initiation of the Mediterranean Messinian salinity crisis, but the longer-term fall may have been linked to tectonic uplift in the Mediterranean region. Widespread distribution of 'TCC-style' cycles of approximately the same age suggests a regional (Western Mediterranean) or global control on sea-level change responsible for TCC cycles. In addition, four subaerial exposure-capped TCC cycles may correlate with similar subaerial unconformities in the South Pacific, suggesting at least a partial eustatic control on TCC cyclicity. The high rates of relative sea-level change needed to generate a minimum of 25-30 m sea-level changes associated with each cycle are consistent with glacio-eustacy along with rapid evaporitic drawdown in the Mediterranean. ?? 2001 Elsevier Science B.V. All rights reserved.

Palaeogeography, Palaeoclimatology, Palaeoecology↗

USGS1978

Evaluation of an aerial survey of Pacific walruses

An aerial survey of Pacific walruses ( Odobenus rosmarus divergens ) was evaluated to determine the reliability of estimates of population abundance. The probability of detecting groups of walruses on the pack ice remained uniform to at least 0.93 km from the flight line, whereas the probability of detection decreased significantly beyond 0.23 km for walruses in the water. Walruses were more abundant along the ice-edge zone between 162 and 165°W than in other areas of the Chukchi Sea during September 1975. Few walruses were observed in consolidated pack ice north of the ice-edge zone or in ice-free water to the south. More walrus groups and larger mean group size were observed on September 8 than on other days. We estimated abundance for each day and all days combined using methods based on sample area and numbers of strip samples. Estimates varied among days by over an order of magnitude; this variation is attributed to the combined effect of chance sampling of an aggregated population and variation in the fraction of walruses hauled out. The coefficient of variation of the estimates ranged between 0.25 and 0.99. This imprecision was due to the aggregated distribution of walruses and the large variation in group size. Using the survey data as a basis for stratification, we calculated that, due to the high variability within strata, a sample size of 40% of the total area or 56% of the total available strips would be required to obtain 95% confidence limits within 10% of the estimate of total abundance. Variation contributed by observer error in estimating group size also is relatively unimportant to the precision of abundance estimates. Studies of natural history, particularly those oriented toward activity and habitat selection, would help investigators estimate bias due to the variable fraction hauled out and design surveys based on meaningful strata. Estimates of total abundance based on limited survey efforts will provide information of little reliability.

Journal of the Fisheries Research Board of Canada↗

USGS1964

Water levels in observation wells in Santa Barbara County, California, 1963

The U.S. Geological Survey, in cooperation with the Santa Barbara County Water Agency, continued the study of the ground-water resources of Santa Barbara County (fig. 1) in 1963. As part of the study, the Geological Survey made monthly water-level measurements in 247 wells; 17 of which were equipped with automatic water-level recorders. These measurements and measurements made by the Santa Maria Valley Water Conservation District are included in this report— In addition, the U.S. Bureau of Reclamation measured the water levels in wells along the Santa Ynez River between Cachuma Dam and Rucker Crossing, but the measurements have not been included herein. In addition to the observation-well program, the Geological Survey is preparing interpretive reports on the ground-water conditions in the Ellwood-Gaviota area, the Lompoc and Santa Ynez upland areas of the Santa Ynez River basin, the Santa Barbara-Summerland area, and the Santa Maria Valley. The basic data from which these reports are being prepared can be consulted at the Santa Barbara office of the Geological Survey. This report was prepared by the Geological Survey, Water Resources Division, under the general supervision of Fred Kunkel, district geologist in charge of ground-water investigations In California, and under the immediate supervision of C. P. Zones, geologist in charge of the Santa Barbara subdistrict office. Measurements for the period 1941-55 were published in U.S. Geological Survey water-supply papers; measurements for the period 1956-62 were released locally in duplicated form.' A report by G. A. LaRocque, Jr., and others (1950) contains descriptions of 2,246 wells in the ground-water basins of the county in 1942. It also contains many water-level measurements made before 1942 by the city of Santa Barbara, the Santa Maria Valley Water Conservation District, the San Joaquin Power Division of the Pacific Gas and Electric Co., the Union Sugar Co., the Union Oil Co., and other organizations and individuals. Comprehensive reports on the geology and ground-water resources of the Santa Ynez River basin (Upson, Thomasson, and others, 1951; Wilson, 1959), the south-coast basins (Upson and others, 1951), the Santa Maria Valley area (Worts, 1951), the Cuyama Valley (Upson and Worts, 1951) and the San Antonio Creek valley (Muir; 1964) were published as Geological Survey water-supply papers. A report on stream runoff and ground-water storage capacity of the Santa Ynez River valley (Troxell and Wilson, 1952) was released to the open file in October 1952. A complete bibliography of reports of investigations made by the Water Resources Division, U.S. Geological Survey, in Santa Barbara County since 1940 is included in this report.

California↗

USGS2025

Revised length categories and standard weight equation for Northern Pikeminnow

Objective Length and weight indices (e.g., proportional size distribution, relative weight) provide standardized benchmarks that are useful for comparing groups of fish, identifying ecological interactions, and evaluating the effect of management actions. However, the current length categories and standard weight ( W s ) equation for Northern Pikeminnow Ptychocheilus oregonensis , a species of important management focus in the Pacific Northwest, were developed using limited data, unclear methods, and no validation. As such, we sought to revise the length categories and W s equation for Northern Pikeminnow. Methods We used the all-tackle world record to develop length categories for Northern Pikeminnow. We compiled data from 100,663 Northern Pikeminnow from 114 populations in Idaho, Montana, Oregon, Washington, and British Columbia to develop a revised W s equation. Most fish were measured in fork length (FL), so we converted total lengths (TLs) to FLs using the equation TL = −2.301 + 0.916(FL); r 2 = 0.998. We used the regression line percentile, linear empirical percentile (EmP), and quadratic EmP methods to develop 50th percentile and 75th percentile W s equations. We then assessed length-related biases in our W s equations and the previously published equation. Results We propose minimum FLs of 17 cm (7 inches; stock), 26 cm (10 inches; quality), 35 cm (14 inches; preferred), 41 cm (16 inches; memorable), and 51 cm (20 inches; trophy) for proportional size distribution calculations. The previously published W s equation exhibited substantial length-related biases according to the Willis and weighted empirical quartile method tests. The EmP 50th-percentile W s equation was the only equation that we evaluated that did not exhibit length-related bias. The EmP 50th-percentile W s equation was the best performing equation (i.e., no length-related bias detected). The equation is log 10 ( W s ) = −5.258 + 3.135(FL), where W s is in grams and FL is in millimeters. The equation is valid for Northern Pikeminnow 90–580 mm FL. Conclusion The length categories, length conversion, and W s equation presented here will aid fisheries professionals in the study and management of Northern Pikeminnow populations.

British Columbia, Idaho, Montana, Oregon Washingto↗

USGS2010

Geologic map of the Bartlett Springs Fault Zone in the vicinity of Lake Pillsbury and adjacent areas of Mendocino, Lake, and Glenn Counties, California

The Lake Pillsbury area lies in the eastern part of the northern California Coast Ranges, along the east side of the transform boundary between the Pacific and North American plates (fig. 1). The Bartlett Springs Fault Zone is a northwest-trending zone of faulting associated with this eastern part of the transform boundary. It is presently active, based on surface creep (Svarc and others, 2008), geomorphic expression, offset of Holocene units (Lienkaemper and Brown, 2009), and microseismicity (Bolt and Oakeshott, 1982; Dehlinger and Bolt, 1984; DePolo and Ohlin, 1984). Faults associated with the Bartlett Springs Fault Zone at Lake Pillsbury are steeply dipping and offset older low to steeply dipping faults separating folded and imbricated Mesozoic terranes of the Franciscan Complex and interleaved rocks of the Coast Range Ophiolite and Great Valley Sequence. Parts of this area were mapped in the late 1970s and 1980s by several investigators who were focused on structural relations in the Franciscan Complex (Lehman, 1978; Jordan, 1975; Layman, 1977; Etter, 1979). In the 1980s the U.S. Geological Survey (USGS) mapped a large part of the area as part of a mineral resource appraisal of two U.S. Forest Service Roadless areas. For evaluating mineral resource potential, the USGS mapping was published at a scale of 1:62,500 as a generalized geologic summary map without a topographic base (Ohlin and others, 1983; Ohlin and Spear, 1984). The previously unpublished mapping with topographic base is presented here at a scale of 1:30,000, compiled with other mapping in the vicinity of Lake Pillsbury. The mapping provides a geologic framework for ongoing investigations to evaluate potential earthquake hazards and structure of the Bartlett Springs Fault Zone. This geologic map includes part of Mendocino National Forest (the Elk Creek Roadless Area) in Mendocino, Glenn, and Lake Counties and is traversed by several U.S. Forest Service Routes, including M1 and M6 (fig. 2). The study area is characterized by northwest-trending ridges separated by steep-sided valleys. Elevations in this part of the Coast Ranges vary from 1,500 ft (457 m) to 6,600 ft (2,012 m), commonly with gradients of 1,000 ft per mile (90 m per km). The steep slopes are covered by brush, grass, oak, and conifer forests. Access to most of the area is by county roads and Forest Service Route M6 from Potter Valley to Lake Pillsbury and by county road and Forest Service Route M6 and M1 from Upper Lake and State Highway 20. From the north, State Highway 261 provides access from Covelo. Forest Service Route M1 trends roughly north from its intersection with Route M6 south of Hull Mountain and through the Elk Creek and Black Butte Roadless areas to State Highway 261. Side roads used for logging and jeep trails provide additional access in parts of the area.

Open-File Report↗

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↗

USGS2006

Environmental threats to tidal-marsh vertebrates of the San Francisco Bay estuary

The San Francisco Bay and delta system comprises the largest estuary along the Pacific Coast of the Americas and the largest remaining area for tidal-marsh vertebrates, yet tidal marshes have been dramatically altered since the middle of the 19th century. Although recent efforts to restore ecological functions are notable, numerous threats to both endemic and widespread marsh organisms, including habitat loss, are still present. The historic extent of wetlands in the estuary included 2,200 km2 of tidal marshes, of which only 21% remain, but these tidal marshes comprise >90% of all remaining tidal marshes in California. In this paper, we present the most prominent environmental threats to tidal-marsh vertebrates including habitat loss (fragmentation, reductions in available sediment, and sea-level rise), habitat deterioration (contaminants, water quality, and human disturbance), and competitive interactions (invasive species, predation, mosquito and other vector control, and disease). We discuss these threats in light of the hundreds of proposed and ongoing projects to restore wetlands in the estuary and suggest research needs to support future decisions on restoration planning.

Studies in Avian Biology↗

USGS2011

Hydrogeologic framework and groundwater/surface-water interactions of the Chehalis River basin, Washington

The Chehalis River has the largest drainage basin of any river entirely contained within the State of Washington with a watershed of approximately 2,700 mi 2 and has correspondingly diverse geology and land use. Demands for water resources have prompted the local citizens and governments of the Chehalis River basin to coordinate with Federal, State and Tribal agencies through the Chehalis Basin Partnership to develop a long-term watershed management plan. The recognition of the interdependence of groundwater and surface-water resources of the Chehalis River basin became the impetus for this study, the purpose of which is to describe the hydrogeologic framework and groundwater/surface-water interactions of the Chehalis River basin. Surficial geologic maps and 372 drillers' lithostratigraphic logs were used to generalize the basin-wide hydrogeologic framework. Five hydrogeologic units that include aquifers within unconsolidated glacial and alluvial sediments separated by discontinuous confining units were identified. These five units are bounded by a low permeability unit comprised of Tertiary bedrock. A water table map, and generalized groundwater-flow directions in the surficial aquifers, were delineated from water levels measured in wells between July and September 2009. Groundwater generally follows landsurface-topography from the uplands to the alluvial valley of the Chehalis River. Groundwater gradients are highest in tributary valleys such as the Newaukum River valley (approximately 23 cubic feet per mile), relatively flat in the central Chehalis River valley (approximately 6 cubic feet per mile), and become tidally influenced near the outlet of the Chehalis River to Grays Harbor. The dynamic interaction between groundwater and surface-water was observed through the synoptic streamflow measurements, termed a seepage run, made during August 2010, and monitoring of water levels in wells during the 2010 Water Year. The seepage run revealed an overall gain of 56.8 ± 23.7 cubic feet per second over 32.8 river miles (1.7 cubic feet per second per mile), and alternating gains and losses of streamflow ranging from -48.3 to 30.9 cubic feet per second per mile, which became more pronounced on the Chehalis River downstream of Grand Mound. However, most gains and losses were within measurement error. Groundwater levels measured in wells in unconsolidated sediments fluctuated with changes in stream stage, often within several hours. These fluctuations were set by precipitation events in the upper Chehalis River basin and tides of the Pacific Ocean in the lower Chehalis River basin.±

Scientific Investigations Report↗

USGS2022

Geologic field-trip guide to volcanism and its interaction with snow and ice at Mount Rainier, Washington

Mount Rainier is the Pacific Northwest’s iconic volcano. At 4,393 meters and situated in the south-central Cascade Range of Washington State, it towers over cities of the Puget Lowland. As the highest summit in the Cascade Range, Mount Rainier hosts 26 glaciers and numerous permanent snow fields covering 87 square kilometers and having a snow and ice volume of about 3.8 cubic kilometers. It remains by far the most heavily glacier-clad mountain in the conterminous United States despite having lost about 14 percent of its ice volume between 1970 and 2008. Five major rivers head at Mount Rainier—the White, Carbon, Puyallup, Nisqually, and Cowlitz Rivers. Because Mount Rainier is situated west of the Cascade Range crest, all of these rivers eventually turn and drain westward. The Puget Lowland, situated west to northwest of Mount Rainier, is the Pacific Northwest’s most densely populated area, including Seattle, Tacoma, and Olympia. The Puget Lowland is now home to a population of more than 4.5 million and a vibrant economy. Mount Rainier is one of the most hazardous volcanoes in the United States, not so much because of its explosivity, but rather because of its frequent eruptions, its propensity to produce voluminous far-traveled lahars, and its proximity to large population centers of the Puget Lowland. Steep-sided, glacially carved valleys serve as lahar conduits, and even mild eruptions commonly produced large lahars that traveled into areas now populated by hundreds of thousands of people. This guide describes a five-day field trip to view the geology of Mount Rainier as it relates to volcanism and its interaction with snow and ice. Day 1 will focus on lahars in the White River valley. We will drive to Enumclaw, Washington, to begin the day then work our way back upvalley toward Mount Rainier. Day 2 concentrates on geology of the Sunrise-Glacier Basin area within Mount Rainier National Park. As part of day 2 activities, we will hike about 10 miles from Sunrise to the top of Burroughs Mountain, down into Glacier Basin, and be picked up at White River Campground. On day 3 we will pack up and move to Paradise, stopping to examine geology along Stevens Canyon Road. We will hike from Paradise along the Golden Gate Trail and eventually eastward to the former Paradise Ice Caves area (the ice caves have melted out). Day 4 involves hiking from Comet Falls trailhead to Mildred Point and return (~7 miles; 11 km), examining geology along the way. During the first half of day 5, we will visit sites on the south side of Mount Rainier to study lahar deposits, then return to the tour origin.

Washington↗

USGS2003

Icelandic-type crust

Numerous seismic studies, in particular using receiver functions and explosion seismology, have provided a detailed picture of the structure and thickness of the crust beneath the Iceland transverse ridge. We review the results and propose a structural model that is consistent with all the observations. The upper crust is typically 7 ?? 1 km thick, heterogeneous and has high velocity gradients. The lower crust is typically 15-30 ?? 5 km thick and begins where the velocity gradient decreases radically. This generally occurs at the V p ??? 6.5 km s-1 level. A low-velocity zone ??? 10 000 km2 in area and up to ??? 15 km thick occupies the lower crust beneath central Iceland, and may represent a submerged, trapped oceanic microplate. The crust-mantle boundary is a transition zone ???5 ?? 3 km thick throughout which V p increases progressively from ???7.2 to ???8.0 km s-1. It may be gradational or a zone of alternating high- and low-velocity layers. There is no seismic evidence for melt or exceptionally high temperatures in or near this zone. Isostasy indicates that the density contrast between the lower crust and the mantle is only ???90 kg m-3 compared with ???300 kg m-3 for normal oceanic crust, indicating compositional anomalies that are as yet not understood. The seismological crust is ???30 km thick beneath the Greenland-Iceland and Iceland-Faeroe ridges, and eastern Iceland, ???20 km beneath western Iceland, and ???40 km thick beneath central Iceland. This pattern is not what is predicted for an eastward-migrating plume. Low attenuation and normal V p/V s ratios in the lower crust beneath central and southwestern Iceland, and normal uppermost mantle velocities in general, suggest that the crust and uppermost mantle are subsolidus and cooler than at equivalent depths beneath the East Pacific Rise. Seismic data from Iceland have historically been interpreted both in terms of thin-hot and thick-cold crust models, both of which have been cited as supporting the plume hypothesis. This suggests that the plume model for Iceland is an a priori assumption rather than a hypothesis subject to testing. The long-extinct Ontong-Java Plateau, northwest India and Parana??, Brazil large igneous provinces, beneath which mantle plumes are not expected are all underlain by mantle low-velocity bodies similar to that beneath Iceland. A plume interpretation for the mantle anomaly beneath Iceland is thus not required.

Geophysical Journal International↗

USGS2025

Shortening migration by 4500 km does not affect nesting phenology or increase nest success for black brant (Branta bernicla nigricans) breeding in Arctic and subarctic Alaska

Background Since the 1980s, Pacific Black Brant ( Branta bernicla nigricans , hereafter brant) have shifted their winter distribution northward from Mexico to Alaska (approximately 4500 km) with changes in climate. Alongside this shift, the primary breeding population of brant has declined. To understand the population-level implications of the changing migration strategy of brant, it is important to connect movement and demographic data. Our objectives were to calculate migratory connectivity, a measure of spatial and temporal overlap during the non-breeding period, for Arctic and subarctic breeding populations of brant, and to determine if variation in migration strategies affected nesting phenology and nest survival. Methods We derived a migratory network using light-level geolocator migration tracks from an Arctic site (Colville River Delta) and a subarctic site (Tutakoke River) in Alaska. Using this network, we quantified the migratory connectivity of the two populations during the winter. We also compared nest success rates among brant that used different combinations of winter sites and breeding sites. Results The two breeding populations were well mixed during the winter, as indicated by a migratory connectivity score close to 0 (− 0.06) at the primary wintering sites of Izembek Lagoon, Alaska (n = 11 brant) and Baja California, Mexico (n = 48). However, Arctic birds were more likely to migrate the shorter distance to Izembek (transition probability = 0.24) compared to subarctic birds (transition probability = 0.09). Nest survival for both breeding populations was relatively high (0.88–0.92), and we did not detect an effect of wintering site on nest success the following year. Conclusions Nest survival of brant did not differ among brant that used wintering sites despite a 4500 km difference in migration distances. Our results also suggested that the growing Arctic breeding population is unlikely to compensate for declines in the larger breeding population of brant in the subarctic. However, this study took place in 2011–2014 and wintering at Izembek Lagoon may have greater implications for reproductive success under future climate conditions.

Movement Ecology↗

USGS2004

Twentieth century demographic changes in cirio and cardón in Baja California, Mexico

Aim&ensp; Our purpose was to discern long-term large-scale patterns of survivorship and recruitment of two dominant, charismatic and useful desert plants, cirio [Fouquieriaceae; Fouquieria columnaris (Kell.) Kell. ex Curran] and cardón [Cactaceae; Pachycereus pringlei (S.Watson) Britton & Rose], and to evaluate the effects of physical and human factors. Location&ensp; The study included 77 sites distributed over c. 13,200 km 2 in the northern Vizcaíno Region of the Sonoran Desert, state of Baja California, México. Method&ensp; Censuses used identified individuals ( n = 3780 cirio and 2246 cardón) and were based on repeat photography. Time intervals between censuses ranged from 29 to 96 years, ending in 1996–2002. Earlier repetition (1963) of old photographs at 14 sites allowed analysis of temporal variation. The effect of elapsed time was modelled with Weibull functions for survivorship and linear functions for recruitment. To explain the residual variations, we tested categorical and continuous variables related to substrate, geomorphology, climate and geography. Human impacts were weighed with historical and quantitative analysis. Results&ensp; Elapsed time accounted for 45% of the variation of survivorship in cirio but only 35% in cardón. The fitted Weibull curves were used to estimate longevity: all-size cohorts of 1000 individuals would die out in 388 (cirio) and 723 years (cardón). Recruitment in cirio was linearly related to time ( r 2 = 0.71) and averaged < 0.003 year −1 but was less than mortality at 90% of the sites. For cardón, recruitment averaged > 0.005 year −1 , was linearly related to time ( r 2 = 0.66) and was less than mortality at only 33% of the sites. Vital rates were not strongly correlated between mid- and late-century but were mostly similar to the long-term regional rates. Removing the factor of elapsed time, the residual variations showed that survivorship was greater on sites protected from winds for cirio and was less on very coarse soils for cardón. Recruitment increased with latitude in cirio and was greater on southern exposures for both species. The residual variations were not clearly affected, at a regional scale, by other factors thought to be important, including elevation, distance to the Pacific Ocean, geology, slope gradient, soil stability, older vs. young alluvial soils, and soil Ca : Mg and Na : K ratios. Human impacts have been sporadic and heterogeneous but locally strong; our quantitative indices of accessibility did not show regionally significant effects. Blowdown by hurricanes is a sporadic cause of major mortality for cirio but not necessarily for cardón. Main conclusions&ensp; At our scales, effects of time outweigh those of substrate, and human impact was scant. Large patterns were pronounced: cirio experienced a prolonged, widespread decline in the 1900s, while cardón fluctuated in different directions and degree among local populations. Cirio was found to be inherently much shorter-lived than cardón. We also suggest that recruitment in cirio was low due to long periods with relatively dry winters that affected the entire region, while spatial heterogeneity of cardón recruitment seemed more related to the variation in summer rains.

Journal of Biogeography↗

USGS2007

Longitudinal patterns of fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River, Oregon

The Lower Crooked River is a remarkable groundwater-fed stream flowing through vertical basalt canyons in the Deschutes River Valley ecoregion in central Oregon (Pater and others, 1998). The 9-mile section of the river between the Crooked River National Grasslands boundary near Ogden Wayside and river mile (RM) 8 is protected under the National Wild and Scenic Rivers Act (16 U.S.C. 1271-1287) for its outstandingly remarkable scenic, recreational, geologic, hydrologic, wildlife, and botanical values (ORVs), and significant fishery and cultural values. Groundwater springs flow directly out of the canyon walls into the Lower Crooked River and create a unique hydrologic setting for native coldwater fish, such as inland Columbia Basin redband trout (Oncorhynchus mykiss gairdneri). To protect and enhance the ORVs that are the basis for the wild and scenic designation, the Bureau of Land Management (BLM) has identified the need to evaluate, among other conditions, fish presence and habitat use of the Lower Crooked River. The results of this and other studies will provide a scientific basis for communication and cooperation between the BLM, Oregon Water Resources Department, Oregon Department of Fish and Wildlife (ODFW) and all water users within the basin. These biological studies initiated by the BLM in the region reflect a growing national awareness of the impacts of agricultural and municipal water use on the integrity of freshwater ecosystems. Biological surveys are needed to better understand the aquatic ecosystem of the Lower Crooked River. This baseline information will be valuable to public land managers whose task is to balance resource use while protecting the unique attributes (that is, ORVs) of the Lower Crooked River. The habitat requirements of coldwater fishes in this section of stream are of particular interest due to state and federal regulation of water temperature in order to protect and restore fish populations. Historical data on the distribution and abundance of stream fishes in the Lower Crooked River are limited to point observations by fishermen and local biologists because steep canyon walls have limited access to most of the river. Surveys of aquatic habitat (channel morphology and substrate composition) have been conducted for the BLM by the ODFW (Oregon Department of Fish and Wildlife, 1997), U.S. Forest Service (United States Forest Service, 2003), and the U.S. Fish and Wildlife Service (USFWS), but fish surveys using electrofishing gear have never been conducted in the isolated 11-mile section of the Crooked River Gorge, and visual observations with mask and snorkel have only been made at isolated point locations where hiking trails provide access to the river (K. Jones, Steve Marx, and Brett Hodgson, ODFW; P. Lickwar, USFWS; pers. comm.). Thus, there is a poor understanding of stream fish presence and distribution throughout Lower Crooked River. Information on fish assemblages is available for the Deschutes River basin and applies generally to the Lower Crooked River because the two rivers were connected historically (Zimmerman and Ratliff 2003). The construction of dams throughout the Deschutes River basin has eliminated historic runs of salmon and steelhead and prevented migration of bull trout and Pacific lamprey into the Crooked River system. Native fish species expected to occur in the Lower Crooked River include Columbia Basin redband trout ( Oncorhynchus mykiss gairdneri ), mountain whitefish ( Prosopium williamsoni ), sculpin ( Cottus spp.), two species of dace ( Rhinichthys spp.), two species of sucker ( Catostomus spp.), northern pikeminnow ( Ptychocheilus oregonensis ), chiselmouth ( Acrocheilus alutaceus ), and redside shiner ( Richardsonius balteatus ). Threespine stickleback ( Gasterosteus aculeatus ), a species native to western Oregon, also occurs in the basin but is believed to be introduced (D. Markle, Department of Fisheries and Wildlife, Oregon State University, personnel commun.). Extensive stocking of rainbow trout has contributed to a large population of naturalized fish of hatchery origin in the Lower Crooked River. Due to the difficulty of differentiating between wild redband trout and naturalized rainbow trout of hatchery origin, the general classification of rainbow trout ( Oncorhynchus mykiss ) is used throughout this report to describe the fish that were observed in the Lower Crooked River. Exotic fish species expected to occur in the Lower Crooked River include large- and smallmouth bass ( Micropterus spp.), yellow perch ( Perca flavescens ), and brown bullhead (Ameiurus nebulosis) (Zimmerman and Ratliff 2003). The goal of this project was to examine longitudinal patterns in fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River during summer conditions. Specific objectives were to (1) characterize the spatial distribution of native and non-native fishes, (2) describe variation in channel morphology, substrate composition, and water temperature, and (3) evaluate the associations between fishes, aquatic habitat, and water temperature.

Oregon↗