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At least 613 records · Page 34Linked to original sources
USGS2026

Transcriptional changes in wild Yukon River Chinook Salmon associated with Ichthyophonus infections

Objective We compared differentially expressed genes in Chinook Salmon Oncorhynchus tshawytscha with three divergent Ichthyophonus statuses (undetected, subclinical infections, or clinical disease; n = 100) to investigate associated transcriptomic responses. Disease associated with the fish parasite Ichthyophonus sp. was first diagnosed in adult Chinook Salmon from the Yukon River in the late 1980s and has subsequently been implicated in premature host mortality. Methods Chinook Salmon tissue sample collections and Ichthyophonus infection data were leveraged from a multi-agency collaboration during summer 2022 at three locations along the main-stem Yukon River that spanned nearly 2,000 km of freshwater migration (lower, middle, and upper river). We sequenced the transcriptome and compared this to infection status based on routine diagnostic procedures. Results Among the 17,569 genes for which messenger RNA was detected, we identified a transcription signature in the skeletal muscle that was associated with Ichthyophonus infections and included 53 differentially expressed genes. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction—all processes that are known to be influenced by senescence during spawning migrations. Conclusions Results demonstrate a clear transcriptional difference between diseased fish (clinical disease group) and those in which Ichthyophonus was undetected, including identifying candidate markers for infection in this population. These results provide a foundation for development of nonlethal biomarkers to evaluate potential Ichthyophonus infections in Chinook Salmon based on gene transcription, protein products, or gene variants (e.g., polymorphisms).

Journal of Aquatic Animal Health↗
USGS2026

Review of Bayesian dynamic occupancy models and the implications of incomplete sampling

One popular tool for modeling long-term wildlife monitoring data is the dynamic occupancy model. Dynamic occupancy models require detection/non-detection observations recorded during repeated visits to the same site across many seasons. However, sampling all sites repeatedly for multi-year studies is not always possible due to limited funding, sites being difficult to access, the addition of sites after monitoring has begun, or even global pandemics. We explore the ramifications of incomplete sampling of sites across seasons on the modeling of dynamic occupancy data. We review four popular choices for modeling dynamic occupancy data, then, with simulation, we explore the implications of incomplete sampling on the inferences gleaned from the different models. These models are also fit to a data set monitoring American Bullfrog breeding populations along the Yellowstone River floodplain in Montana, USA. Results from the bullfrog data analyses are consistent with the results from the simulation, and help support our modeling conclusions. Ideally, if there are no limitations on data collection, we suggest repeatedly visiting all sites in all seasons, however this is often difficult, or impossible for a variety of reasons. For data already collected, regardless of incomplete sampling, we suggest using the dynamic or auto-logistic models.

Montana↗
USGS2026

A sea ice entrapment event in the southern Chukchi Sea: Analysis and prediction

Amplified Arctic warming is reducing sea ice cover, which is driving an increase in geopolitical interest in the region as it offers the possibility of reducing shipping times between Asia, Europe, and eastern North America, at the risk of increased ice hazards. Here, we examine the case of the Norseman II research ship that was trapped by sea ice in the southern Chukchi Sea for 14 days in June 2024. This is the first study of its sort in this region. We show that anomalously thick and extensive sea ice was present north of the region prior to the event, and that strong northerly winds in early June advected this ice southward, trapping the ship. Later in June, southerly winds advected ice northwards away from the ship, helping to free it. We further show that the event was forecastable.

Alaska↗
USGS2026

Role of volcano-tectonic interactions during early-phase magma-assisted continental rifting

We study volcanic-tectonic interactions during the early phase of rifting in the Natron Rift, a magmatic segment of the East African Rift System. We use the open-source crustal deformation modeling code, PyLith, to model deflation during the 2007–2008 explosive eruptions and inflation during 2016–2023. We compare predictions of surface displacements resulting from magma reservoir inflation from 3D models with and without topography and homogeneous and heterogeneous material properties against Global Navigation Satellite System displacements from 2016 to 2023. We prefer the model with heterogeneous material properties and topography for fitting the observed displacements. Including topography improves the fit to GNSS data and modulates stress changes from shallow magma sources. Our numerical modeling of Coulomb stress changes suggests that deflation of a magma reservoir under the active Ol Doinyo Lengai volcano could trigger oblique normal slip on the Natron Fault with Coulomb stress increases exceeding ∼0.1 MPa on the volcano-adjacent fault segment. Fault slip on the Natron Fault is less likely during inflation of the magma reservoir because normal compressive stress increases on the fault. We also demonstrate that Coulomb stress changes are sensitive to the inclusion of topography in our model, particularly because the depth of the magma reservoir is similar to the amplitude of the topographic relief.

Ol Doinyo Lenga↗
USGS2026

Geochemistry of the 2022 Mauna Loa eruption: A comparison with earlier historical summit reservoir eruptions, with implications for magma supply and recharge

On November 28th, 2022, following a record historical repose period of 38 years, Mauna Loa erupted about 145 × 10 6 m 3 of lava and tephra over a 15-day period. The eruption was confined to the summit caldera region and the upper Northeast Rift Zone and is remarkably homogeneous in composition in both time and space. In these respects, it is typical of prior shallow summit reservoir magma bodies, recently estimated to be at a depth of around 1–2 km beneath the caldera. In contrast with these earlier magma bodies, which typically contain 6.7–7.1% MgO and are perched at the low-MgO end of olivine-control trends, the 2022 lava and tephra are more evolved with 6.24 + / − 0.03% MgO. This implies a temperature difference of around 11 °C with the prior 1984 magma. The simplest explanation is that over 38 years, cooling and crystallization of the remaining 1984 magma body has significantly exceeded magma recharge, giving rise to the evolved 2022 magma. The problem with this model is that we know from a variety of geophysical observations that in those 38 years, Mauna Loa has been erratically inflating, with heightened periods since around 2000 attributed to magma recharge. To reconcile these differences, we suggest instead that the 1984 magma cooled and crystallized much more extensively, from 1166 °C to around 1106 °C, co-crystallizing plagioclase, clinopyroxene, pigeonite and subsequently enstatite instead of pigeonite. At this point, the residual 1984 magma would have an MgO content around 4.2% and been about 50% solidified. Subsequent recharge and mixing by dominantly reservoir magmas, derived from a deeper 3–4-km intermediate magma reservoir, eventually produced the 2022 magma.

Hawaii↗
USGS2026

Loss and transformation of coastal wetlands due to global change in the conterminous United States: Past, present, and future

Coastal wetlands are being transformed by global change, impacting the ecological and societal benefits provided by these ecosystems. Synthesizing knowledge of historical and expected future transformations in coastal wetlands can help inform forward-looking planning and stewardship efforts. Here, we review anticipated future ecological transformations in coastal wetlands of the conterminous United States and contrast them with past transformations. We examine trends at the national scale but focus in detail on the following six wetland-rich regions: (1) Everglades, (2) Mississippi River delta, (3) Chesapeake Bay, (4) San Francisco Estuary, (5) Puget Sound, and (6) Great Lakes. This review is among the first to integrate and compare coastal wetland transformations in the Great Lakes with their oceanic counterparts. Between 1850 and 1970, wetland losses across the nation were high because coastal wetlands were viewed as flooded wastelands needing to be drained, filled, or excavated to make room for other land uses. Over the last 50 years, growing public and scientific appreciation of the ecological and societal benefits provided by coastal wetlands has fostered tremendous gains in wetland restoration and legal protection. Looking to the future, climate change and accelerated sea-level rise have become critical threats to coastal wetlands and are emerging as major drivers of ecological loss and transformation. This review synthesizes regional knowledge regarding past, present, and future changes to help coastal scientists, environmental managers, and the public better anticipate and prepare for future coastal wetland transformations due to climate change, accelerated sea-level rise, land-use change, and other aspects of global change.

conterminous United States↗
USGS2026

Improved estimates of relative occurrence and abundance using opportunistic surveys and presence-only observations: A zero-inflated integrated species distribution model

Modeling tools for estimating and forecasting shifts in species distributions are becoming increasingly valuable for conservation planning and response. This is especially true for wild bird populations, which have been declining across habitats and regions. Species distribution models (SDM) represent a diverse set of tools with options for addressing various sources of bias. Complex spatial processes associated with rare or clustered species can be accounted for using zero-inflated SDMs, whereas biased survey data can be integrated with additional data sources to improve estimates. Each option addresses an important and common source of bias, but the two SDM frameworks have not been implemented together previously. We present a novel zero-inflated extension of an integrated SDM framework for a Poisson regression (ZI-iSDM), allowing for the estimation of independent occurrence and abundance processes by integrating opportunistic survey and presence-only data. We validated performance of this ZI-iSDM using simulated datasets under different degrees of species rarity and density on the landscape as well as sampling bias in opportunistic datasets. We additionally applied this model to real survey data for multiple wild bird species using publicly available observation data combined with open-access environmental information to describe habitat associations. We found that integrating presence-only data, such as banding or harvest events, can compensate for potential deficiencies in opportunistic surveys by expanding sampling to be more representative of available and used habitat. Additionally, models that first differentiated occurrence and abundance using a ZI term were better suited for approximating distributions of spatially clustered species.

Ecological Modeling↗
USGS2026

A practical framework for GT-seq panel optimization

Genotyping-in-thousands by sequencing (GT-seq) panels are powerful tools in ecological, evolutionary and conservation genomics, yet the optimization process critical for robust and reproducible genotyping remains poorly formalized. Here, we present an iterative workflow for GT-seq panel optimization that emphasizes systematic refinement, quality control and structured decision-making to improve panel performance across diverse populations and study contexts. We illustrate this framework through the development and optimization of a GT-seq panel for white-tailed deer, a widely distributed and ecologically important North American species. From an initial set of 1200 candidate SNPs selected from a commercial microarray (OVSNP60, containing 72,728 SNPs) and prioritized for high heterozygosity, primers were designed for 646 loci. The final optimized panel contains 508 high-performing markers retained after iterative removal of overamplifying primer pairs, adjustment of primer concentrations, PCR conditions and bioinformatic filtering. The overall proportion of SNPs with more than 70% genotype rate increased from 25.5% in the first optimization round to 87.8% in the final round. Consequently, the overall genotype rate increased from 39.4% to 84%. We also identify key quality-control checkpoints and practical criteria to guide panel refinement and ensure consistent performance. By prioritizing optimization as an integral component of GT-seq panel development, this work provides a reproducible framework for generating robust, high-throughput genotyping tools in non-model species and underscores the importance of iterative refinement to maximize data quality and utility.

Molecular Ecology Resources↗
USGS2026

Bee-ing similar: Low diversity, no population structure, and signals of adaptation in two North Dakota bumble bees

Habitat fragmentation and destruction are driving widespread declines in ecosystem function, species abundance, and genetic diversity across the globe. Among the affected taxa are bumble bees (genus Bombus ), which are essential pollinators. Bumble bee declines have been linked to anthropogenic pressures such as land-use change and climate change. To better understand how the environment is shaping bumble bee populations, we employed a landscape genetics approach to examine the genetic diversity, population structure, and potential local adaptation of two widespread species— Bombus ternarius and Bombus griseocollis —across North Dakota. From 2017–2020, 161 B. ternarius and 200 B. griseocollis bumble bees were sampled in ND across 13 and 17 sites, respectively. We found low levels of heterozygosity and inbreeding across all populations for both species, with no evidence of population structure or isolation by distance. Our results revealed signatures of potential local adaptation to climatic variables and land cover characteristics, suggesting that our species are adapted to environmental gradients across the state. Having similar results between both species across all analyses suggests that other wide-ranging bumble bees in the region may share these patterns. High connectivity can buffer short-term population losses, but low genetic diversity may constrain adaptive potential and reduce resilience to future environmental change and emerging threats. Our findings have broad applicability to other pollinators and taxa facing similar environmental pressures. Both species have populations that continually exchange genes creating widespread connectivity but are still locally shaped by adaptation.

North Dakota↗
USGS2026

Dormant-season prescribed fires can enhance forage quality for two growing seasons in the northwestern Great Plains

Fire is an ecological disturbance that can accelerate nutrient cycling and alter herbivore distribution in grasslands and shrublands. Historically and today, humans have used prescribed fire to enhance forage quality for wild and domestic herbivores, and to achieve other management objectives. Contextual factors such as ecosystem type, seasonality, and fuel characteristics can determine how prescribed fire affects forage quality. For example, forage quality enhancements are relatively short lived in shortgrass steppe and subhumid grasslands but may persist for multiple years in northern mixed-grass prairie and sagebrush steppe. Outcomes near ecosystem boundaries are uncertain. Using 152 independent, small-plot, prescribed burns completed over multiple years at 36 sites in Wyoming and South Dakota, USA, we tested the effects of ecosystem type (northern mixed-grass prairie vs. sagebrush grassland ecotone), burn seasonality (fall vs. spring), and fuel characteristics (ambient vs. added fuel) on forage quality. Across ecosystems, fall fires had strong positive effects on forage quality parameters during the first growing season after fire, and energy benefits that persisted into the second growing season after fire. In northern mixed-grass prairie, spring and fall prescribed fires implemented before the same growing season yielded similar forage quality enhancements for one season. Finally, artificially increased fuel loads had few effects on forage quality. Although forage quality rarely dropped below critical nutrition thresholds for ruminants regardless of burning, our findings suggest relatively consistent, positive forage quality responses to prescribed fire across ecosystem types, seasonality of dormant-season burns, and fuel characteristics. Many improvements lasted through one growing season, and some persisted into a second growing season. Managers could take advantage of short-term nutritional benefits via adaptive management strategies that allow animals access to burned and unburned areas.

South Dakota, Wyoming↗
USGS2026

Temperate wetlands lose climate-cooling capacity under warming

Temperate inland wetlands have long been viewed as climate regulators, with sustained CO₂ sequestration offsetting continuous CH₄ emissions over centennial–millennial timescales. However, the net climatic effect of these opposing fluxes remains uncertain under anthropogenic warming as they differ in both magnitude and atmospheric lifetime. We combine 19,000 CH₄ chamber measurements from 202 temperate inland wetlands with carbon burial rates from 16 dated sediment cores in North America’s Prairie Pothole Region to estimate greenhouse gas dynamics over two centuries. Here we show that CH₄ emissions rise by ~1.39 kg CH₄ ha⁻¹ yr⁻¹ over the historical period and are projected to approach 950 kg CH₄ ha⁻¹ yr⁻¹ under high-forcing scenarios by 2100, while CO₂ sequestration is expected to decline by ~0.3 kg CO₂ ha⁻¹ yr⁻¹, driving a shift toward persistent net CO₂-equivalent source behaviour and a weakening of the long-term cooling effect that wetlands have provided under natural conditions.

Prairie Pothole Region↗
USGS2026

CrustCheck: A conceptual framework for interpreting biocrust trait–function relationships in drylands

Introduction Biocrusts are increasingly recognized for their contribution to soil stability, hydrology, nutrient cycling, and energy balance in drylands, yet practical field methods for assessing functional roles are limited. Existing approaches typically rely on cover estimates, taxonomic identification, or laboratory analyses, providing little insight into functional variation among biocrust types. To address this gap, we developed CrustCheck, a literature-derived conceptual framework that synthesizes potential relationships between easily observable biocrust traits and key ecological functions. The framework provides a foundation for future empirical validation of these relationships. Objectives We aimed to: (1) identify visual characteristics of biocrusts potentially associated with key ecological functions, and (2) synthesize these relationships into a literature-derived conceptual framework for comparative interpretation of potential biocrust contributions to landscape function. Methods We conducted a structured review of global literature on biocrusts' contribution to landscape function, drawing on multiple databases, targeted journals, and identifying relevant scientific publications from reference lists. We screened sources for information on relationships between visual traits and metrics of landscape function, synthesized relationships thematically, and used them to develop a multi-trait, function-oriented conceptual framework to inform further testing of these hypotheses in the field. Results Our review revealed that visual traits such as thickness/height, patchiness, cover, and surface roughness emerged as potential indicators of surface stability, hydrological function, and nutrient accumulation. Community composition was also frequently associated with these functions, while color reflected energy balance and carbon fixation potential. Conclusions Literature reveals that visual traits of biocrusts may serve as proxies for landscape function. CrustCheck is presented here as a conceptual synthesis framework intended to support interpretation of potential trait–function relationships rather than as a quantitatively validated predictive tool.

Restoration Ecology↗
USGS2026

Bat skin microbiome and the association of ecoregion and bat species that impacted isolation of members with bioactivity against Pseudogymnoascus destructans

Background Microbiome constituents can serve as a primary defense against vertebrate pathogens. This may be crucial to the protection of North American bats who have been devastated over the last two decades by the fungal pathogen, Pseudogymnoascus destructans (Pd) , which causes white-nose syndrome (WNS). The objectives of this study were to isolate members of the external microbiome of bats post-hibernation in Arizona and New Mexico before the arrival of WNS, to identify those bacteria with bioactivity against Pd , and to determine the variables associated with antifungal strains. Results In this study we isolated 2,936 bacteria from the fur and skin of 314 bats across 12 bat species at 6 sites across New Mexico and Arizona from 2013 to 2016. Selective media were used to promote the isolation of Actinomycetota (2,594 isolates, 88.4%), particularly species of Streptomyces (2,045 isolates, 69.7%) known for their bioactivity. Although Actinomycetota isolation was targeted, this collection includes representatives from Pseudomonadota (Alpha-, Beta -, and Gamma-Proteobacteria ), Bacillota , and Bacteroidota phyla also common to the bat microbiome. A bi-layer challenge assay performed on 1,089 isolates identified 61 bat-associated bacteria with activity against Pd. These results were pooled with efforts by Hamm et al. [ 1 ] to determine what metrics impacted isolation of bacteria that inhibit Pd ( n = 97). Ecoregion and bat species were determinant variables associated with Pd inhibition. Conclusions This study represents, to our best knowledge, the largest culture collection of bacteria from bats’ skin and fur before the impact of WNS. We identified bacteria with antifungal activity against Pd and found significant associations of bioactive strains with bat species and ecoregions.

Arizona, New Mexico↗
USGS2026

Thermal infrared and ultraviolet remote sensing of sulfur dioxide gas emitted during the 2018 lower East Rift Zone eruption of Kilauea, Hawaiʻi

Ultraviolet (UV) remote sensing is widely used to detect volcanic sulfur dioxide (SO₂) due to its high sensitivity and favorable spatial and temporal resolution. However, significant discrepancies have been reported between ground-based and satellite-based UV observations of dense volcanic plumes. A notable example is the 2018 lower East Rift Zone eruption of Kīlauea, where SO₂ emission rates derived from ground-based Differential Optical Absorption Spectroscopy (DOAS) measurements differed substantially from those obtained by the spaceborne Tropospheric Monitoring Instrument (TROPOMI). In this study, we investigate these differences by applying thermal infrared (TIR) satellite retrievals using a modified version of the SO₂-ALTA algorithm to Moderate Resolution Imaging Spectroradiometer (MODIS) observations. The resulting TIR-derived SO₂ fluxes are compared with ground-based DOAS data, satellite UV observations, and petrological estimates of gas emissions. Our results show strong agreement between TIR-derived fluxes, ground-based DOAS measurements, and petrological estimates, particularly during the peak and plateau phases of the eruption. In contrast, satellite UV-derived SO₂ emissions are systematically lower. We find that TIR observations are more effective in quantifying high-concentration SO₂ plumes in the near-vent region, while UV measurements are more sensitive under lower-concentration conditions but more affected by scattering in optically dense plumes. These findings highlight the complementary strengths of UV and TIR remote sensing techniques and emphasize the importance of accounting for plume density and observation geometry when interpreting satellite SO₂ retrievals.

Hawaii↗
USGS2026

Mid-Cretaceous porphyritic magmatism in the Beartooth Mountains of the northern Laramide foreland and its connection to Frontier Formation sediment dispersal in Bighorn basin, Montana-Wyoming (USA), and Cordilleran tectonism

Porphyritic intrusions in the southeast Beartooth Mountains and porphyritic cobbles from the Torchlight conglomerate of the Cenomanian Frontier Formation in Bighorn basin (Montana-Wyoming, USA) bear striking resemblance. We utilize geologic mapping, petrography, geochemistry, and geochronology to characterize rocks from both locations and test whether the Beartooth Mountains area was the provenance for Bighorn basin cobbles. Mapping on Line Creek Plateau in the Beartooth Mountains shows three units with porphyritic phenocrysts consisting dominantly of plagioclase, plagioclase + potassium feldspar, and plagioclase + quartz. Petrography shows embayed quartz, opacitic rims, and zoned plagioclase. Geochemistry characterizes the intrusions as trachydacite to trachyte and trace elements exhibit enrichment in light rare earth elements and slight depletion in heavy rare earth elements relative to primitive mantle. Zircon U-Pb dating shows substantial Archean inheritance and ca. 104−92 Ma dates; some samples display multiple mid-Cretaceous date populations. Bighorn basin porphyritic cobbles exhibit similar modal mineralogy, near-identical geochemistry, and Archean inheritance and mid-Cretaceous geochronology. We suggest the porphyritic cobbles were sourced from basement-hosted porphyritic intrusions now exposed in the Beartooth Mountains, given that geochemistry does not agree with coeval volcanic sources along the Frontier Formation depositional fairway (Idaho batholith) or sedimentary-hosted Beartooth Mountains porphyritic sills intruded into Cambrian shale. Stratigraphic evidence does not support kilometer-scale mid-Cretaceous Beartooth Mountains exhumation to expose basement-hosted porphyritic intrusions, and we therefore present a volcanic hypothesis to bring rocks to the surface. This mid-Cretaceous multimillion-year magmatism is unexplained by tectonic models for the north-central Laramide foreland, and thus we further explore the emplacement processes, spatiotemporal significance, and tectonic implications of these rocks.

Montana, Wyoming↗
USGS2026

Cascadia Subduction Zone science: Call for the next generation community seismic velocity model

The Cascadia subduction zone (CSZ) hosts major seismic and tsunami hazards, yet key questions persist about the relationship between margin structure, fluid distribution, episodic tremor and slip, shallow megathrust behavior, shaking and tsunamigenesis, and the resulting hazard estimates. Addressing these problems requires an empirically grounded, three‐dimensional seismic velocity model to illuminate subsurface structure and properties and to provide a basis for geophysical studies such as earthquake simulations and ground‐motion estimation. In May 2024, the National Science Foundation‐funded Cascadia Region Earthquake Science Center (CRESCENT) community velocity model (CVM) working group, with U.S. Geological Survey and regional partners, convened a workshop to identify priorities for such a model. Participants emphasized the features necessary for addressing key science questions, including implementing findability, accessibility, interoperability, and reusability (FAIR) access, capturing along‐strike and along‐dip structural heterogeneity, resolving shallow offshore–onshore structure, constraining elastic properties and quantifying their uncertainties for numerical wave propagation simulations, their validation benchmarks, and supporting associated accurate earthquake ground‐motion simulations and hazard assessments. This article describes the priorities defined in the workshop, and a description of how, guided by these needs, CRESCENT plans to develop multiple generations of a CVM to advance CSZ science and improve seismic and tsunami hazard modeling across the Pacific Northwest. The CVM will span the CSZ from the surface to ∼100 km depth, offshore and east of the Cascades into Idaho (∼132°–110° W) and the southern and northern tectonic regime transitions (∼36°–52° N) to capture the entire tectonic system as well as its surroundings.

Cascadia Subduction Zone↗