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Nonstationary demographic state-space models using unreplicated counts for species undergoing environmental stressors

A fundamental task in ecological statistics is to estimate abundance and growth rate distributions from wildlife monitoring data to inform conservation management. Modeling time series of wildlife populations presents a number of challenges from both statistical and ecological perspectives, including discreteness; lack of replication; nonstationarity; and observation, demographic, and other phenomenological processes. Nonstationary dynamics are often exhibited by populations undergoing environmental stressors. Models must account for these characteristics to produce reliable estimates of abundance and trends, yet estimation can be challenging with unreplicated data. We propose nonstationary demographic state-space models using unreplicated counts for populations undergoing environmental stressors. A reduced growth rate model matches the complexity of the unreplicated count data, and a fecundity bound on growth rate distributions allows the separation of processes affecting growth rates like environmental stressors from those affecting abundance external to growth rates like migration. NDSSMs allow for the embedding of nonstationary model components, and we explore the use of changepoints, volatility clustering, and migration processes. We apply the proposed nonstationary models in case studies of herons affected by predator/competitor reestablishment and three bat species affected by a fungal pathogen causing white-nose syndrome. Nonstationary models outperform stationary models and generalized linear mixed effects models according to model scoring and visual inspection of predictions, and provide estimates more consistent with published values. Incorporating migration improves model fit universally, even with approximate one-way immigration, most likely because populations are extirpated, recolonized, and increase multiple-fold over the upper bound set by species fecundity. In addition, estimates of the timing and severity of the environmental stressor differed for models with migration. Including nonstationary and demographic components in a fecundity-bounded growth rate model improves inference and benefits interpretability of hyperparameters. In turn, this adjusts uncertainties in predictions of abundance and growth rates over time, providing the ingredients needed for informed conservation analysis and for directing future monitoring of at-risk species.

Journal of Agricultural, Biological and Environmen

Coastal and Marine Hazards and Resources Program decadal science strategy 2020–2030

Overview The decadal science strategy of the Coastal and Marine Hazards and Resources Program (CMHRP) of the U.S. Geological Survey for 2020 to 2030 describes the CMHRP's vision and mission and the strategic framework needed to support key program goals: Conduct research and develop science-based tools that lead to safer, more productive coastal communities and improved stewardship of natural resources.

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Coastal Science Navigator companion guide—Discover the U.S. Geological Survey coastal science products you need

The Coastal Science Navigator is an online gateway to a wide variety of U.S. Geological Survey (USGS) coastal change hazards-related information, data, and tools relevant to stakeholders’ scientific and decision-making needs. The products within the Coastal Science Navigator provide data related to past, present, and future threats to our coastlines. The filter search allows users to see all available products and identify relevant options by time scale, geographic scope, coastal hazard theme, and other filters. The guided search suggests products based on users’ answers to a short series of questions. A comprehensive summary is available for each product. The idea for the Coastal Science Navigator arose in 2020 in response to stakeholder feedback identifying the need for a central source for USGS coastal science information. It was published in July 2023 and initially included 55 products. Regular updates are planned to integrate other existing and new products. This guide introduces some of the many coastal change hazards-related products available through the USGS. In it, we showcase the products included in the Coastal Science Navigator’s initial publication in July 2023. While it is not representative of all the information, tools, and data available, we hope it serves as a compelling snapshot of what the USGS has to offer and encourages you to explore the Coastal Science Navigator to discover more of the products you need. To navigate this guide, the products have been organized by the time scale they are best suited for—past, present, or future—although many products cover multiple time scales. An additional section features software, one of the many product types available as filters within the Coastal Science Navigator. Other products include downloadable data, websites, and geonarratives (web pages that combine text, images, and interactive maps into narratives you can scroll through). Featured geographic scopes are also highlighted within this guide, detailing some of the many regions in which the USGS conducts research and illustrating another way to filter products within the Coastal Science Navigator.

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Decadal shifts in groundwater age detected by environmental tracers across California, USA

Groundwater age offers important insight into recharge, storage, and contamination risk. Although models predict age changes can be driven by pumping and climate variability, direct observational evidence remains limited. Here, we analyzed paired environmental tracer suites (tritium, carbon-14, and tritiogenic helium-3) collected a decade apart from 268 wells across California to assess the prevalence of groundwater age transience. Travel-time distribution models and statistical tests indicated age transience at 29% of sites, occurring most often in agricultural regions, such as the San Joaquin Valley and Southern Coast Ranges, where large carbon-14 changes coincided with substantial nitrate and chloride shifts. Sites with tritiogenic helium-3 data showed more frequent age transience, underscoring the value of multi-tracer data sets. These results provide the first regional evidence of widespread groundwater age change and a method for detecting changing water balances with implications for groundwater sustainability and water quality.

California

Bioconcentration of per- and polyfluoroalkyl substances and precursors in fathead minnow tissues environmentally exposed to aqueous film-forming foam-contaminated waters

Exposure to per- and polyfluoroalkyl substances (PFAS) has been associated with toxicity in wildlife and negative health effects in humans. Decades of fire training activity at Joint Base Cape Cod (MA, USA) incorporated the use of aqueous film-forming foam (AFFF), which resulted in long-term PFAS contamination of sediments, groundwater, and hydrologically connected surface waters. To explore the bioconcentration potential of PFAS in complex environmental mixtures, a mobile laboratory was established to evaluate the bioconcentration of PFAS from AFFF-impacted groundwater by flow-through design. Fathead minnows ( n = 24) were exposed to PFAS in groundwater over a 21-day period and tissue-specific PFAS burdens in liver, kidney, and gonad were derived at three different time points. The ∑PFAS concentrations in groundwater increased from approximately 10,000 ng/L at day 1 to 36,000 ng/L at day 21. The relative abundance of PFAS in liver, kidney, and gonad shifted temporally from majority perfluoroalkyl sulfonamides (FASAs) to perfluoroalkyl sulfonates (PFSAs). By day 21, mean ∑PFAS concentrations in tissues displayed a predominance in the order of liver > kidney > gonad. Generally, bioconcentration factors (BCFs) for FASAs, perfluoroalkyl carboxylates (PFCAs), and fluorotelomer sulfonates (FTS) increased with degree of fluorinated carbon chain length, but this was not evident for PFSAs. Perfluorooctane sulfonamide (FOSA) displayed the highest mean BCF (8700 L/kg) in day 21 kidney. Suspect screening results revealed the presence of several perfluoroalkyl sulfinate and FASA compounds present in groundwater and in liver for which pseudo-bioconcentration factors are also reported. The bioconcentration observed for precursor compounds and PFSA derivatives detected suggests alternative pathways for terminal PFAS exposure in aquatic wildlife and humans.

Environmental Toxicology and Chemistry

Woods Hole Coastal and Marine Science Center—2023 annual report

The 2023 annual report of the U.S. Geological Survey Woods Hole Coastal and Marine Science Center highlights accomplishments of 2023, includes a list of 2023 publications, and summarizes the work of the center, as well as the work of each of its science groups. This product allows readers to gain a general understanding of the focus areas of the center’s scientific research and learn more about specific projects and progress made throughout 2023, all while enjoying photographs taken in various environments and laboratories, and applicable maps and figures.

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Woods Hole Coastal and Marine Science Center—2024 annual report

The 2024 annual report of the U.S. Geological Survey Woods Hole Coastal and Marine Science Center highlights accomplishments of 2024, includes a list of 2024 publications, and summarizes the work of the center, as well as the work of each of its science groups. This product allows readers to gain a general understanding of the focus areas of the center’s scientific research and learn more about specific projects and progress made throughout 2024, all while enjoying photographs taken in various environments and laboratories, and applicable maps and figures.

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Enhanced geothermal systems electric-resource assessment for the Great Basin, southwestern United States

The U.S. Geological Survey recently (2025) completed a provisional assessment of the geothermal-electric resources associated with high-temperature, low-permeability rock formations of the Great Basin, Southwestern United States. If sufficient technological advances to commercialize enhanced geothermal systems occur, then a current best provisional estimate for electric-power generation capacity of 135 gigawatts electric are available from the upper 6 kilometers of the Earth’s crust. This estimate is a potential substantial increase of the installed geothermal electricity-generating capacity from <1 to 10 percent of current total U.S. power production capacity.

California, Idaho, Nevada, Oregon, Utah

Near-surface geophysics: Environmental applications

The field of geophysics encompasses a broad and diverse compilation of methodologies that employs principles of physics to characterize properties of earth materials within the subsurface. While geophysical methods have a long history in resource exploration and studies of Earth’s interior, the subdiscipline of “near-surface geophysics” has evolved in recent decades for examination of the shallow, near-surface environment for a range of purposes ranging from archaeological or forensic investigations to assessment of geologic, hydrologic, biologic, and geochemical properties and processes. “Environmental geophysics” are near-surface geophysical studies and methods that focus on understanding natural systems (e.g., watershed hydrology, groundwater–surface water connections, biophysical processes) as well as research pertaining to anthropogenic impacts and land management, (e.g., contamination and remediation, saltwater intrusion, agricultural practices). This field can be further subdivided into subdisciplines focused on specific topics and applications, such as water resources and hydrology (hydrogeophysics) or biologic and microbial processes (biogeophysics). Studies in environmental geophysics span a range of scales, from pore-scale laboratory tests to watershed-scale or regional field experiments. Methods vary by the nature of physics employed, the specific measurement acquired, and how that data is ultimately processed and analyzed to produce interpretable results. There exists further diversity in the acquisition logistics, geometry, and timing of data collection. Geophysical data can be collected in boreholes (one-dimensional, 1-D, vertical profiles), along survey lines (two-dimensional, 2-D, cross-sections), or in dense sensor arrays or gridded profiles (three-dimensional, 3-D, models). Regarding the temporal aspect, studies can conduct one-time geophysical surveys to obtain detailed imaging of subsurface structure or use timelapse and continuous monitoring to investigate variations in subsurface properties over time. The cumulation of all possible permutations of these factors (method, acquisition geometry, survey design, and target application) results in an immense diversity among environmental geophysical studies. Nevertheless, this field remains unified in the pursuit of understanding natural and human-impacted near-surface environments through geophysical investigations. Here we highlight some key references within environmental geophysics. Resources on geophysical theory, acquisition logistics, processing and inversion workflows, and example case studies are categorized into the most common geophysical classes within Geophysical Methods. Lastly, example references for the dominant types of applications in environmental geophysical studies are catalogued in Environmental Applications.

Book chapter

The U.S. Geological Survey, the U.S. Department of Defense, and the U.S. Intelligence Community—100 years of mapping and remote sensing collaboration, 1879–1979

Introduction The U.S. Geological Survey (USGS)—a Federal civilian agency—and U.S. military and intelligence agencies collaborate on mapping and remote sensing and have since the establishment of the USGS. The organizations exchange data and information and share technology to further their respective missions in service to the American people. Often referred to as examples of “good government” or “whole of government,” the collaboration avoids costly duplication and maximizes time and effort for the government sectors. Collaboration between these sectors started with the original mapping of the United States and evolved to include remote sensing after the advent of aerial photography and satellite imagery.

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Trends and environmental impacts of virtual water trade

Virtual water describes water embedded in the production of goods and offers meaningful insights about the complex interplay between water, trade and sustainability. In this Review, we examine the trends, major players, traded products and key drivers of virtual water trade (VWT). Roughly 20% of water used in global food production is traded virtually rather than domestically consumed. As such, agriculture dominates VWT, with livestock products, wheat, maize, soybean, oil palm, coffee and cocoa contributing over 70% of total VWT. These products are also driving VWT growth, the volume of which has increased 2.9 times from 1986 to 2022. However, the countries leading VWT contributions (with China, the United States, the Netherlands, Germany and India accounting for 34% of the global VWT in 2022) have remained relatively stable over time, albeit with China becoming an increasingly important importer. VWT can mitigate the effects of water scarcity and food insecurity, although there are concerns about the disconnect between consumers and the environmental impacts of their choices, and unsustainable resource exploitation. Indeed, approximately 16% of unsustainable water use and 11% of global groundwater depletion are virtually traded. Future VWT analyses must consider factors such as water renewability, water quality, climate change impacts and socioeconomic implications.

Nature Reviews Earth & Environment

Bayesian mapping of regionally grouped, sparse, univariate earth science data

Some earth science data are naturally grouped by region, and it is often desirable to map these data by region. However, if there are only a few samples within each region, then the map should be smoothed in an appropriate way to mitigate the problems that arise from having only a few samples. A smoothing algorithm based on a Bayesian hierarchical model is developed and presented in this report. This algorithm has several features that make it especially suitable for mapping earth science data: it can account for measurements that are censored, it can process multiple datasets with different measurement errors and different censoring thresholds, and it can calculate the uncertainty in any statistic that is mapped. The algorithm is demonstrated by mapping gold concentrations that are measured in streambed sediments in the Taylor Mountains quadrangle in southwestern Alaska.

Alaska

Engineering and risk research—A strategic vision for extending USGS earthquake science to risk assessment and mitigation

As a part of the U.S. Geological Survey (USGS) Natural Hazards Mission Area, the Engineering and Risk Project (ERP) of the Geologic Hazards Science Center conducts civil engineering research to extend natural hazards science to risk assessments. The ERP includes predominantly, but not exclusively, staff funded by the USGS Earthquake Hazards Program. A major focus of the ERP is to deliver actionable information to decisionmakers that helps promote the safety, security, and economic well-being of the Nation. The report discusses briefly the ERP’s evolution and scope, its organization structure, describes key products and deliverables, their efforts to engage with external partners, and its strategy and vision in conducting range of engineering and risk research. The research topics outlined in this report, as developed by the ERP, may be used to facilitate project planning activities during the next 10 years and serve as a longer-term planning resource for the USGS Earthquake Hazards Program and Geologic Hazards Science Center.

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U.S. Geological Survey—Department of the Interior, Region 11, Alaska—2023–24 biennial science report

Introduction U.S. Geological Survey (USGS) Mission—The USGS national mission is to monitor, analyze, and predict the current and evolving dynamics of complex human and natural Earth-system interactions and to deliver actionable information at scales and timeframes relevant to decision makers. Consistent with the national mission, the USGS in Alaska provides timely and objective scientific information to help address issues and inform management decisions across five interconnected focus areas: Energy and Minerals; Geospatial Mapping; Natural Hazards; Water Quality, Streamflow, and Ice Dynamics; and Ecosystems. The USGS in Alaska consists of approximately 350 scientists and support staff working in 3 Alaska-based science centers. USGS science activities are also initiated by the Cooperative Research Unit and USGS centers outside Alaska. In the last 5 years, USGS research in Alaska has produced many scientific benefits resulting from more than 900 publications. Publications relevant to Alaska can be conveniently searched by keyword through the USGS Publications Warehouse at https://pubs.usgs.gov/.

Alaska

Assessing environmental drivers of denitrification in restored riverine floodplains

Restoration of impaired floodplains is an increasingly prevalent strategy for alleviating water quality concerns and reducing downstream flooding at watershed scales. Floodplains temporarily store water and slow flow velocity to promote sedimentation during overbank flooding and remove inorganic nitrogen from floodwater and groundwater via denitrification. Evaluating the impacts of different restoration strategies on denitrification can inform more strategic investments into floodplain modifications that improve water quality outcomes. Our research investigates how denitrification rates in floodplains respond to environmental factors that are actionable from an engineering perspective through design and water resources management. We seasonally measured soil denitrification enzyme activity and various environmental characteristics in 4 floodplains with different restoration design and management approaches at the confluence of the Wabash and Tippecanoe Rivers in Indiana, United States. Our results showed that denitrification rates in an agricultural floodplain were significantly lower than in restored floodplains with native vegetation. Certain soil conditions characteristic of floodplain wetlands were associated with higher denitrification, particularly elevated total nitrogen, moisture, silt, and organic matter contents. Vegetation species composition was correlated with denitrification rates. This link may reflect the direct effects of vegetation on soil conditions, such as supplying labile organic carbon, or indirect effects, such as vegetation acting as an indicator of hydrologic regime and land use. Denitrification seasonally varied, peaking in winter when nitrate supply from rivers draining agricultural watersheds in the region is also high. Substrate limitation of soil denitrification enzyme activity was most significant during the summer when overbank flooding, which replenishes soil nitrogen stocks, rarely occurs. Our findings indicate that denitrification capacity will likely be maximized in riverine floodplains that are restored as wetlands with diverse native vegetation and enhanced hydrologic connectivity. Such restoration activities promote higher denitrification rates via elevated moisture, fine sediment deposition, and soil organic matter.

Tippecanoe River, Wabash River

State of science, gap analysis, and prioritization for southeastern United States water-quality impacts from coastal storms—Fiscal year 2023 program report to the Water Resources Mission Area from the Water Availability Impacts of Extreme Events Program—Hurricanes

Tropical cyclones (coastal storm events that include tropical depressions, tropical storms, and hurricanes) cause landscape-scale disturbances that can lead to impaired water quality and thus reduce water availability for use. Stakeholders and scientists at local and national scales have illustrated a need for understanding these risks to water quality. A regional and comprehensive understanding of the impacts of tropical storms and hurricanes on surface-water and groundwater quality—and thus water availability—is lacking for potentially impacted coastal and inland areas. As the U.S. Geological Survey considers development of tools to predict the extent to which water-quality impacts of hurricanes affect water availability, an assessment of the state of the science of hurricane impacts is needed, including a gap analysis and prioritization of data and science needs. This assessment focuses on the southeastern coastal States.

southeastern United States

Low-frequency earthquakes track the motion of a captured slab fragment

Accurate tectonic models are essential for assessing seismic hazard and fault interactions. However, the plate configuration at the complex Mendocino triple junction, where the San Andreas Fault and the Cascadia subduction zone meet, remains uncertain. We analyzed fault slip associated with a recently identified zone of tectonic tremor and low-frequency earthquakes (LFEs) near the southern edge of the subducting Gorda slab. Based on tidal sensitivity and P-wave first motions, we show that the LFEs are generated by dipping, strike-slip motion. This suggests that a former Farallon slab fragment, now captured by the Pacific plate, is translating northward beneath westernmost North America. This geometry effectively extends the slab interface fault, challenging prevailing interpretations of slab window formation and creating a potential unaccounted earthquake hazard in this region.

Science

Re-Os geochronology of molybdenite by LA-ICP-MS/MS

Re-Os geochronology is a powerful tool to directly date sulphide mineralisation using phases such as molybdenite, pyrite and chalcopyrite. We present a snapshot of a method in development utilizing laser ablation inductively coupled-plasma ‘triple quad’ mass spectrometry (LA-ICP-MS/MS) for Re-Os geochronology of molybdenite. While traditional LA-(MC)-ICP-MS measurements are limited by the >90% isobaric interference correction of parent radioactive 187 Re on radiogenic daughter 187 Os, the MS/MS technology minimizes this correction through careful instrument tuning and use of a (CH 4 + H 2 + He) reaction gas mixture to mass shift 187 Os away from 187 Re. We demonstrate the potential of the MS/MS technique by presenting robust Re-Os dates for three different molybdenite samples ranging in age from ~28 to 1520 Ma.

Conference Paper