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USGS2025

Linking stream-reach nitrogen loads and groundwater “reachsheds” to inform wastewater-nitrogen management actions, Cape Cod, Massachusetts

Study Region Cape Cod, Massachusetts, U.S.A. Study Focus Anthropogenic nitrogen (N) is a key factor in degrading groundwater and surface-water quality, particularly in coastal New England where onsite wastewater systems are prevalent. This study evaluated whether direct N-load measurements in streams on Cape Cod, Massachusetts, coupled with flow-path information from groundwater-flow models, can effectively identify potential land areas where nitrogen mitigation could substantially reduce loads to receiving waters. Nitrogen fluxes were measured along 63 stream reaches during winter and summer and paired with simulated groundwater recharge areas to identify and rank potential areas for reduction of nonpoint-source N inputs. New Hydrologic Insights for the Region Reach-scale nitrate-N loads ranged from −39.1–1182 kg-N/yr per 100 m of stream, indicating spatially variable groundwater inputs across seasons. “Reachsheds” — areas contributing groundwater recharge to specific stream reaches — were delineated using a regional groundwater-flow model. Strong correlations were found between observed N loads and land-use characteristics, especially the number of septic systems and total N inputs from the sum of considered sources. Observed N loads were moderately correlated with recharge area size and wastewater flow estimates. Correlating reach-specific groundwater N loads with land use and parcel-scale nitrogen-yield data identified reachsheds with the highest potential for N load reduction. This approach enables targeted implementation of restoration efforts to optimize nutrient management and support regional load reduction.

Massachusetts↗
USGS2025

‘The fish that stop’: Drivers of historical decline for Pacific cod and implications for modern management in an era of rapidly changing climate

n the Gulf of Alaska, a series of marine heat waves depleted Pacific cod ( Gadus macrocephalus ) biomass to the lowest abundance ever recorded and led to the fishery’s closure in 2020. Although the fishery has been productive for decades, this collapse may have historical precedents. Traditional knowledge holders refer to cod as ‘the fish that stop’, and there is a suggested period of decline in the 1930s. Here we conduct a catch reconstruction of the early commercial fishery (1864–1950), confirming a rapid catch decline in the 1920s and 1930s. Next, we evaluate evidence for possible drivers. We document changes to demand and technology that contributed to declining catch. However, we also find both qualitative and quantitative evidence of depletion, suggesting catch declines were not driven entirely by social factors. Overfishing may have contributed to localized catch declines as evidenced by declining catch rates in heavily fished localities. We also find evidence for climate as a driver of regional decline, with the period of catch decline characterized by up to 2°C higher temperatures as compared to the earlier period of high fisheries production. Our analysis underscores the importance of understanding long-term drivers of fisheries productivity and the value of linking fisheries and climate histories.

Alaska↗
USGS2026

Evaluation of best management practices at an edge-of-field site in the Eagle Creek watershed, Ohio, 2012–20

In 2010, the U.S. Geological Survey worked in partnership with the Great Lakes Restoration Initiative and the Natural Resources Conservation Service to identify farm fields in priority watersheds—watersheds critically important to Great Lake health. Intensive best management practices were implemented in five States to test the efficacy of best management practices, also referred to as agricultural conservation practices, to reduce sediment and nutrient runoff on agricultural fields. These fields were chosen as representatives of the priority watersheds because their farming practices and geographical conditions were common among farms in those watersheds. A farm site located near Findlay, Ohio, in the Eagle Creek watershed used two conservation practices, cover crop (Natural Resources Conservation Service practice standard 340) and variable rate technology (VRT; Natural Resources Conservation Service practice standard 590), which represent common practices in the Maumee priority watershed. This study monitored surface runoff and subsurface tile runoff at the Eagle Creek watershed site. The effects of cover crop and VRT nutrient application on sediment and nutrient runoff were assessed from October 2012 to September 2020. Cover crops were applied in fall of 2016, 2017, and 2018, coinciding with VRT applications. The following parameters were analyzed as part of the study: runoff discharge; peak discharge; and concentrations and loads of total phosphorus, particulate phosphorus, dissolved reactive phosphorus, and suspended sediment. High peak runoff events disproportionally affected nutrient concentrations and loads in runoff. A threshold of the 85th percentile of the peak discharge was chosen to assess the effect of cover crop and VRT nutrient application on nutrient mitigation at each gage. Runoff events below the 85th percentile were considered small, and runoff events over the 85th percentile were considered large. Concentrations from collected water-quality samples were used for the analysis; estimated concentrations were excluded from the statistical evaluation. All surface runoff parameters during small runoff events, except surface runoff volume, were significantly lower in the period with cover crops and VRT implementation. Contrarily, subsurface runoff parameters during small events were not statistically different between the periods with and without cover crops and VRT implementation. Surface and subsurface parameters during large events were also not statistically different between the periods with and without cover crops and VRT implementation. These results indicate cover crops and VRT may improve water quality during small runoff events, but additional best management practices that mitigate large runoff events may lead to greater water-quality improvement given the contribution of large events to overall losses.

Ohio↗
USGS2026

Rewilding the upper Klamath River Basin: Rapid recolonization of Chinook salmon following the world’s largest dam removal

Habitat fragmentation is a global driver of decline in biodiversity, yet evaluations of ecological response following re-connection remain rare. In 2024, four hydroelectric dams on the Klamath River were removed, reconnecting over 640 km of anadromous habitat and marking the largest dam removal project completed to date. We used a stationary high-resolution multi-beam imaging SONAR to quantify adult Chinook salmon ( Oncorhynchus tshawytscha ) passage into newly reopened reaches during the first two migratory seasons following dam removal. An estimated 7,742 (95% CI: 7,702–7,778) Chinook salmon migrated upstream in 2024 and 13,310 (95% CI: 12,876–13,733) in 2025, representing 18–19% of fish returning to the Klamath River Basin. Within this period, Chinook salmon recolonized 88% of their documented historical distribution, expanding into 345 km of reconnected habitats and reaching elevations of up to 1,250 m. Recolonization required fish to swim through dam removal sites, complex hydraulic corridors and engineered fishways, demonstrating the propensity for rapid recolonization at basin scale despite these challenges. These findings provide the first quantitative assessment of salmon response to the world’s largest dam removal and demonstrate how reconnection can catalyze large-scale recolonization in historically fragmented river networks.

California, Oregon↗
USGS2024

A conceptual framework to assess post-wildfire water quality: State of the science and knowledge gaps

Wildfire substantially alters aquatic ecosystems by inducing moderate to catastrophic physical and chemical changes. However, the relations of environmental and watershed variables that drive those effects are complex. We present a Driver-Factor-Stressor-Effect (DFSE) conceptual framework to assess the current state of the science related to post-wildfire water-quality. We reviewed 64 peer-reviewed papers using the DFSE framework to identify drivers, factors, stressors, and effects associated with each study. A total of five drivers were identified and ranked according to their frequency of occurrence in the literature: atmospheric processes > fire characteristics > ecologic processes and characteristics > land surface characteristics > soil characteristics. Commonly reported stressors include increased nutrients, runoff, and sediment transport. Furthermore, although several different factors have been used at least once to explain water-quality effects, relatively few factors outside of precipitation and fire characteristics are frequently studied. We identified several gaps indicating the need for long-term monitoring, multi-factor studies, consideration of organic contaminants, consideration of groundwater, and inclusion of soil characteristics. This assessment expands on other reviews and meta-analyses by exploring causal linkages between influential variables and overall effects in post-wildfire watersheds. Information gathered from our assessment and the framework itself can be used to inform future monitoring plans and as a guide for modeling efforts focused on better understanding specific processes or to mitigate potential risks of post-wildfire water quality.

Water Resources Research↗
USGS2025

The 3D Elevation Program—Supporting Rhode Island’s economy

Introduction High-resolution elevation data are critical to applications of landscape modeling and planning, both of which have a significant effect on Rhode Island’s economy. In these and other enterprises, program managers, while aiming to strike a balance between accuracy and cost, strive to obtain the best available elevation data to help them address a range of issues. Programs focused on climate change, environmental management, transportation design and asset management, aviation navigation and safety, riverine ecosystem management, wildlife habitat characterization and management, shellfish aquaculture, and the management and mapping of forests, parks and recreation areas, soils, wetlands, and impervious surfaces are also among the critical applications that meet the State’s management needs and depend on light detection and ranging (lidar) data that provide a highly detailed three-dimensional (3D) model of the Earth’s surface and aboveground features. The 3D Elevation Program (3DEP) is managed by the U.S. Geological Survey (USGS) in partnership with Federal, State, Tribal, U.S. territorial, and local agencies to acquire consistent lidar coverage at quality level 2 or better to meet the many needs of the Nation and Rhode Island. The status of available and in-progress 3DEP baseline lidar data in Rhode Island is shown in figure 1. 3DEP baseline lidar data include quality level 2 or better, 1-meter or better digital elevation models, and lidar point clouds, and must meet the Lidar Base Specification version 1.2 ( https://www.usgs.gov/3dep/lidarspec ) or newer requirements. The National Enhanced Elevation Assessment identified user requirements and conservatively estimated that availability of lidar data would result in at least $178,560 in new benefits annually to the State. The top 10 Rhode Island business uses for 3D elevation data, which are based on the estimated annual conservative benefits of 3DEP, are shown in table 2.

Rhode Island↗
USGS2025

Groundwater response to managed aquifer recharge at the Southeast Houghton Artificial Recharge Project in Tucson, Arizona

Managed aquifer recharge is a widespread practice for storing water in the subsurface as groundwater. At a managed aquifer recharge facility in southern Arizona, groundwater-level and repeat microgravity data were collected to monitor aquifer response. These data were used to inform parameter identification for an unsaturated-zone flow model used to simulate the recharge process. The facility, the Southeast Houghton Artificial Recharge Project (SHARP), consists of 3 surface basins (about 27,600 square meters [6.8 acres] total surface area) where recycled water is distributed in recharge cycles lasting several months, with dry periods in between. During the study period, December 2020–December 2022, Tucson Water (the City of Tucson’s water utility) reported 6.56×10 6 cubic meters of water (5,320 acre-feet) recharged. Monitoring included groundwater-level observations at 3 monitoring wells and repeat microgravity measurements at as many as 22 locations (some stations were destroyed between surveys). Six gravity surveys were carried out using absolute- and relative-gravity meters. Large gravity increases, more than 250 microgals, were observed during the first repeat survey, 3.5 months after the start of recharge, but only in the immediate vicinity of the recharge basins. Data show that water moved downward to the water table, and storage changes in the unsaturated zone away from the facility were likely minimal. Gravity decreased at stations more than 1 kilometer from the facility, consistent with regional groundwater-level changes. Groundwater-level increases in wells adjacent to the recharge basins began 2 months after the second repeat gravity survey, and 5.5 months after recharge began. Unsaturated-zone flow modeling was carried out using software that simulates water movement and parameter estimation. Model calibration was carried out by minimizing an objective function calculated from the differences between simulated and observed groundwater levels, and between simulated and observed repeat microgravity data. Including repeat microgravity data in the objective function reduced the uncertainty in estimated parameter values for saturated hydraulic conductivity and saturated water content. Modeling indicated that the unsaturated zone between the recharge basins and the water table does not become saturated even after 685 days of simulated infiltration. This gradual wetting may account for increasing infiltration rates over time, as hydraulic conductivity increases with increasing water content. Unsaturated-zone water content decreased rapidly between recharge cycles. Model-simulated groundwater mounding extended about 1 kilometer from the center of SHARP after the 685-day period following the onset of recharge.

Arizona↗
USGS1996

Magnitude and frequency of low flows in the Suwannee River Water Management District, Florida

Low-flow frequency statistics for 20 gaging stations having at least 10 years of continuous record and 31 other stations having less than 10 years of continu ous record or a series of at least two low- flow measurements are presented for unregulated streams in the Suwannee River Water Management District in north-central Florida. Statistics for the 20 continuous-record stations included are the annual and monthly minimum consecutive-day average low- flow magnitudes for 1, 3, 7, 14, and 30 consecutive days for recurrence intervals of 2, 5, 10, 20, and, for some long-term stations, 50 years, based on records available through the 1994 climatic year.Only theannual statistics are given for the 31 other stations; these are for the 7- and 30-consecutive day periods only and for recurrence intervals of 2 and 10 years only. Annual low-flow frequency statistics range from zero for many small streams to 5,500 cubic feet per second for the annual 30- consecutive-day average flow with a recurrenceinterval of 2 years for the Suwannee River near Wilcox (station 02323500). Monthly low-flow frequency statistics range from zero for many small streams to 13,800 cubic feet per second for the minimum 30-consecutive-day average flow with a 2-year recurrence interval for the month of March for the same station. Generally, low-flow characteristics of streams in the Suwannee River Water Management District are controlled by climatic, topographic, and geologic fac tors. The carbonate Floridan aquifer system underlies, or is at the surface of, the entire District. The terrane's karstic nature results in many sinkholes and springs. In some places, springs may contribute greatly to low streamflow and the contributing areas of such springs may include areas outside the presumed surface drainage area of the springs. In other places, water may enter sinkholes within a drainage basin, then reappear in springs downstream from a gage. Many of the smaller streams in the District go dry or have no flow for several months in many years. In addition to the low-flow statistics, four synoptic low-flow measurement surveys were conducted on 161 sites during 1990, 1995, and 1996. The measurements were made to provide "snapshots" of flow conditions of streams throughout the Suwannee River Water Management District. Magnitudes of low flows during the 1990 series of measurements were in the range associated with minimum 7-consecutive-day 50-year recurrence interval to the minimum 7-consecutive-day 20-year recurrence interval, except in Taylor and Dixie Counties, where the magnitudes ranged from the minimum 7-consecutive-day 5-year flow level to the7-consecutive-day 2-year flow level. The magnitudes were all greater than the minimum 7- consecutive-day 2-year flow level during 1995 and 1996. Observations of no flow were recorded at many of the sites for all four series of measurements.

Florida↗
USGS2025

Factors regulating the potential for freshwater mineral soil wetlands to function as natural climate solutions

There are increasing global efforts and initiatives aiming to tackle climate change and mitigate its impacts via natural climate solutions (NCS). Wetlands have been considered effective NCS given their capacity to sequester and retain atmospheric carbon dioxide (CO 2 ) while also providing a myriad of other ecosystem functions that can assist in mitigating the impacts of climate change. However, wetlands have a dual impact on climate, influencing the atmospheric concentrations of both CO 2 and methane (CH 4 ). The cooling effect associated with wetland CO 2 sequestration can be counterbalanced by the warming effect caused by CH 4 emissions from wetlands. The relative ability of wetlands to sequester CO 2 versus emit CH 4 is dependent on a suite of interacting physical, chemical, and biological factors, making it difficult to determine if/which wetlands are considered important NCS. The fact that wetlands are embedded in landscapes with surface and subsurface hydrological connections to other wetlands (i.e., wetlandscapes) that flow over and through geochemically active soils and sediments adds a new layer of complexity and poses further challenges to understanding wetland carbon sequestration and greenhouse gas fluxes at large spatial scales. Our review demonstrates how additional scientific advances are required to understand the driving mechanisms associated with wetland carbon cycling under different environmental conditions. It is vital to understand wetland functionality at both wetland and wetlandscape scales to effectively implement wetlands as NCS to maximize ecological, social, and economic benefits.

Wetlands↗
USGS2025

An inset groundwater-flow model to evaluate the effects of layering configuration on model calibration and assess managed aquifer recharge near Shellmound, Mississippi

The U.S. Geological Survey has developed a high-resolution inset groundwater-flow model in the Mississippi Delta as part of an interdisciplinary collaboration coordinated by the Mississippi Alluvial Plain project to provide a tool that stakeholders can use to support water-resource management decisions. Groundwater withdrawals from the Mississippi River Valley alluvial (MRVA) aquifer have been vital to support agricultural production in the region, but substantial groundwater-level declines near Shellmound, Mississippi, have caused concerns for long-term sustainability of the aquifer. To better understand the subsurface and try to mitigate the long-term groundwater-level declines, stakeholders have undertaken actions including a Groundwater Transfer and Injection Pilot (GTIP) project using a riverbank filtration-based managed aquifer recharge approach. The pilot project consisted of extracting groundwater near the Tallahatchie River and reinjecting it into the aquifer 3 kilometers west where water levels have substantially declined. A high-resolution airborne electromagnetic (AEM) survey was also completed to collect electrical resistivity data to support the GTIP project and the development of the groundwater model. The inset groundwater-flow model was developed to (1) integrate the AEM data into the optimal layering configuration of the MRVA aquifer that the available observation data can support through calibration, and (2) assess the potential effect of the GTIP project on the groundwater levels. The AEM data were processed into three different layering configurations leading to the development of model A (18 layers), model B (16 layers), and model C (8 layers), all at a 100- x 100-meter cell spatial resolution using the U.S. Geological Survey modular finite-difference flow model 6 code with Newton-Raphson formulation. The model development process integrated recent advances in modeling, such as the incorporation of AEM data, the use of outputs from the soil-water-balance (SWB) model, and the Aquaculture and Irrigation Water-Use Model, and was facilitated by robust automation using the open-source python packages Modflow-setup and SFRmaker. Using Parameter Estimation ++ Iterative Ensemble Smoother, the three numerical groundwater-flow models (models A, B, and C) were calibrated against a set of observations, which included aquifer groundwater levels, streamflows, stream stage, and aquifer transmissivity. Results indicate that the detailed representation of MRVA aquifer layers in model A produced the best calibrated model by history matching, and the integration of data representing surficial connectivity played a key role in improving groundwater recharge and enhancing the ability of the model to match groundwater levels in the cone of depression. A forecast model simulated the managed aquifer recharge approach, and the results indicated that, given average irrigation and recharge conditions (2010–15), the GTIP project has the potential to induce groundwater-level increases of as much as 3 meters around the injection site, but a sustained increase would require repetition in subsequent years of water transfer at 2022 rates or above.

Mississippi↗
USGS2024

Monitoring and assessment of urban stormwater best management practices at selected Chicago public schools in Chicago, Illinois, from September 1, 2016, to July 1, 2017

The Space to Grow program helps transform aging and neglected schoolyards of Chicago Public Schools into outdoor community spaces with the goal of promoting health and learning while addressing neighborhood flooding issues. Virgil I. Grissom Elementary School and Donald L. Morrill Math and Science School were selected in 2014 for schoolyard upgrades and the installation of various green infrastructure (GI) improvements. The U.S. Geological Survey installed sensors to measure precipitation, groundwater levels, and stormwater runoff volumes from September 1, 2016, to July 1, 2017. At Virgil I. Grissom Elementary School, about 933,000 gallons of water fell on the schoolyard during the monitoring period. No discharge was recorded coming from the GI sewer lines, but backflow indicated water was flowing from the sewer line draining the impervious running track into the combined manhole structure and backwards into the GI retention basins (as designed). This design allowed for a 100-percent capture rate. Native soil at Virgil I. Grissom Elementary School also was conducive to rapid infiltration. Soil borings at Virgil I. Grissom Elementary School indicated about 10.5 feet (ft) of fine sand overlying silty clay to a depth of at least 16 ft. At Donald L. Morrill Math and Science School, about 1,120,000 gallons of water fell on the schoolyard during the monitoring period. About 72.5 precent of this water was discharged into the sewer system, and the other 27.5 percent was captured by the GI. Unlike Virgil I. Grissom Elementary School, the soil profile at Donald L. Morrill Math and Science School consisted of about 5 ft of clay loam overlying stiff blue clay to a depth of at least 12 ft. The sewer line coming from the GI under the football field was at the bottom of the reservoir. This design seemed to allow water to flow out of the line before being absorbed by the retention basin.

Illinois↗
USGS2025

Land cover change within wetland complexes at Dixie Meadows, Churchill County, Nevada: 2015 – 2023

Dixie Meadows, Nevada, is a system of geothermal springs and seeps that feed a complex of marshes and wetland meadows that are located within lands managed by the Bureau of Land Management (BLM) and the Department of Defense (DOD). A previous U.S. Geological Survey report documented variability in satellite imagery-based land cover classifications for seven wetland complexes at near monthly time intervals between October 2015 and January 2022. This report presents additional data, extending analysis to November 2023. Land cover classifications between October 2015 and November 2023 demonstrated an association between vegetation cover characteristics and surface moisture, with Class 1 having dry, bare soil or sparse upland vegetation, Class 2 having moist, bare soil or sparse to small vegetation, Class 3 having dense green vegetation with potentially saturated soil conditions, Class 4 having a mix of shallow surface water, saturated soil, and dense green vegetation, and Class 5 having open surface water. Most of the wetland complexes occur close to spring outflows primarily within land managed by the DOD, though portions are also within BLM lands. The intervening and surrounding landscape outside of the wetland complexes assessed in this study are managed by the BLM. As a result, Class 1 land covers had the largest areal coverage for BLM managed lands. Classes 2 and 3 land covers were primarily mapped inside the wetland complexes and thus had the largest area coverage within DOD managed lands. Class 4 was almost exclusively mapped within the wetland complexes and thus was largely contained within DOD managed lands. Class 5 (open water) was exclusively mapped in and adjacent to a single wetland complex with catchment ponds on land managed by the BLM. The distribution of these land cover classes over the study period was seasonally and annually variable. Land cover areas of Classes 1 and 2 were larger during the spring months. Conversely, land cover areas of Classes 3 and 4 tended to be greatest during the summer or fall. These patterns might be influenced by differences in seasonal water sources and phenology.

Nevada↗
USGS2024

Cold blood in warming waters: Effects of air temperature, precipitation, and groundwater on Gulf Sturgeon thermal habitats in a changing climate

Objective In a changing climate, the effects of air temperature, precipitation, and groundwater on water temperature and thermal habitat suitability for Gulf Sturgeon Acipenser desotoi , listed as threatened under the U.S. Endangered Species Act, are not well understood. Hence, we incorporated these factors into thermal habitat models to forecast how Gulf Sturgeon may be affected by wide‐ranging climate change scenarios in 2024–2074. Methods Using data from the Choctawhatchee River, Florida, we developed precipitation‐ and groundwater‐corrected air–water temperature models, compared their accuracy with that of conventional air–water temperature models used in fisheries management, and projected future Gulf Sturgeon thermal habitat suitability for normal physiological functioning and fieldwork (i.e., population sampling and telemetry surgeries) in summer (May–August) under 16 climate change scenarios. Result Precipitation‐ and groundwater‐corrected models were more accurate than conventional air–water temperature models (mean improvement in adjusted R 2 = +0.45; range = +0.09 to +0.75). Water temperature was projected to warm at widely variable rates across climate change scenarios encompassing different air temperature, precipitation, and groundwater regimes. Importantly, Gulf Sturgeon summer aggregation areas were cooler and influenced more by precipitation and groundwater and less by air temperature than were non‐aggregation areas. If precipitation and groundwater—as drivers of cooling—become warm in a changing climate, summer aggregation areas were projected to exhibit thermal habitat degradation equivalent to or greater than that of non‐aggregation areas. Conclusion Our results add hydrological context to the premise that aggregation areas provide cool water and energetic savings for Gulf Sturgeon during summer, underscoring the importance of protecting these habitats through groundwater conservation, water quality monitoring, and riparian/watershed habitat management. Our findings indicate that identifying thermally appropriate times for fieldwork activities will be increasingly important and time‐restricted as climate change intensifies. However, our research provides managers with a portfolio of water temperature models and an accurate, cost‐effective, management‐relevant approach to forecasting thermal habitat conditions for Gulf Sturgeon and other species in a changing climate.

Alabama, Florida↗
USGS2025

Hydrologic variability and groundwater age of springs in eastern Oregon and northern Nevada, USA

The ecological importance of springs in semiarid regions is far greater than their small size and sparse distribution, yet little is known about the hydrologic functioning of these systems. During 2016–22, 261 springs were visited in the volcanic terrane of eastern Oregon and northern Nevada. When conditions were suitable, measurements of discharge, water temperature, and specific conductance were made, and samples for the analysis of carbon-14, tritium, and water stable isotopes (WSI) were collected. A subset of 60 springs was revisited during different seasons in the same year and during the dry season in multiple years to evaluate variability in discharge, chemistry, and groundwater age. Specific conductance and WSI varied considerably among springs across the study area but were unexpectedly stable across seasons and years at individual springs. Seasonal and interannual variability in spring discharge was related to the residence time of the discharging groundwater. Springs discharging older groundwater (10 3 –10 4 years) had significantly less variability in their discharge compared to springs discharging younger groundwater (10 0 –10 1 years). Variability among springs discharging younger groundwater included cessation of late-summer discharge at 18 % of the repeat-visit springs. A logistic regression model predicted the age of discharging spring water with 89 % accuracy using only the spring latitude, longitude, elevation, and δ 2 H value. This study framework provides a simple, inexpensive, and robust method to provisionally assess the hydrologic behavior of springs having little or no prior information in understudied, semiarid regions across the globe.

Nevada, Oregon↗
USGS2025

A new groundwater energy transport model for the MODFLOW hydrologic simulator

Heat transport in the subsurface is an important aspect of research related to the effects of a warming climate on ecological services (i.e., cold-water refugia); the development of geothermal resources for energy banking schemes (i.e., aquifer thermal energy storage [ATES]); and the effects of temperature on other aspects of groundwater quality, such as nutrient cycling. Historically, simulation of heat transport using the MODFLOW groundwater simulator and related codes was performed by scaling the input parameters of a solute-transport model to emulate heat transport. However, that approach required additional pre- and post-processing of input and output and could not account for the variation in effective thermal storage and transport properties during transient, unsaturated flow, for example. True heat-transport capabilities in the context of MODFLOW were first introduced in a variant called USG-Transport. More recently, a new groundwater energy-transport (GWE) model type has been added to MODFLOW 6, the core version of the MODFLOW hydrologic simulator. GWE supports the simulation of heat transport on structured or unstructured grids as well as within and between features of advanced packages that represent streams, lakes, multi-aquifer wells, and the unsaturated zone. GWE is integrated within MODFLOW 6 and is accessible through the FloPy Python package and the MODFLOW 6 application programming interface (API). An example simulation demonstrates conduction between grid cells through both the water and the solid aquifer material, including thermal bleeding from saturated overburden cells into a groundwater flow field.

Groundwater↗
USGS2026

A Lake Charr pangenome reveals highly conserved Ohnologs as drivers of phenotypic diversity

Whole-genome duplication (WGD) is hypothesized to spur evolutionary diversification by producing genome-wide duplicate gene sets (Ohnologs) that are initially functionally redundant but can diverge markedly as the effects of relaxed selection accumulate over time. However, the underlying mechanisms remain unclear, in part because genomic studies often reconstruct Ohnolog evolution over millions of years, during which subsequent mutations can obscure deep-time signals. Investigating the relationship between Ohnolog evolution and diversification on a contemporary timescale offers clearer insights. We explore this relationship in Lake Charr ( Salvelinus namaycush ), where ∼10% of genes are retained highly conserved polyploid duplicates following the Salmonid-Specific Fourth Round WGD. Using 31 chromosome-level assemblies of Lake Charr from morphologically and ecologically diverse populations, joined into a pangenome graph, we characterized 189,555 structural variants (SVs) that were significantly less likely to affect genes retained as sequence-conserved Ohnolog pairs, nuancing the hypothesis that gene redundancy, relaxed selection, and functional diversification are intertwined. However, we found that SVs affecting such conserved Ohnologs may be potent drivers of adaptive evolution. Notably, we identified a putative 938-Kb interchromosomal translocation containing 25 genes with highly conserved Ohnologs in a paralogous (but untranslocated) genomic block. This putative translocation appears to have facilitated Ohnolog divergence in ankrd11 and hp , genes putatively linked to craniofacial and lipid metabolic diversity in sympatric Lake Superior morphs. This research reveals that conserved Ohnologs previously presumed to be redundant remain a reservoir for adaptive change.

BioRxiv↗
USGS2026

Northern bobwhites select for native grasses on working grazing land

Northern bobwhite ( Colinus virginianus ; bobwhite) populations have experienced an 85% decline across most of its range since the 1960s. The most drastic decreases have been in the southeastern United States where biologists attribute the decline to widespread habitat loss, including conversion of native grasslands to tall fescue ( Lolium arundinaceum ) and other exotic cool-season grass (CSG) pasture and hayfields. Including agricultural lands in conservation programs could improve habitat conditions on a regional scale. One working-lands conservation strategy involves the use of native warm-season grasses (NWSGs) rather than cool-season exotic grasses as economically viable cattle forage. To evaluate this management practice for creating bobwhite habitat, we conducted a field study on a bobwhite population in eastern Kentucky, USA, where grazed NWSG and burned NWSG fields were adjacent to exotic grazed and exotic hayed CSG fields. Between April 2019 and October 2022, we used radio telemetry to track bobwhites to evaluate resource selection at second- and third-order scales. Bobwhites used traditionally managed CSGs less than would be expected by chance at the second-order scale in both breeding and non-breeding seasons. Bobwhite use of grazed NWSG and burned NWSG was greater than would be expected by chance at the second-order scale in both breeding and non-breeding seasons. Similarly, at the third-order scale, bobwhites used CSGs less than would be expected by chance, whereas NWSGs and woody stems were used more than by chance alone. Our study suggests that bobwhites select NWSGs at multiple spatial scales despite broad-scale availability of managed exotic CSGs. Under a working-lands framework, the integration of NWSGs into working lands could create bobwhite habitat in the southeastern United States, especially if woody stems are present.

Kentucky↗
USGS2026

Light-dependent activity of deepwater sculpin (Myoxocephalus thompsonii) across substrates with and without predation risk

Light availability strongly influences predator–prey interactions in deepwater ecosystems, where visual constraints shape both foraging success and prey behavior. The behavioral response of deepwater sculpin ( Myoxocephalus thompsonii ) to siscowet lake trout ( Salvelinus namaycush siscowet ) was studied under ecologically relevant light intensities spanning several orders of magnitude typical of daytime downwelling light in the 20–100 m depth range of Lake Superior. Trials were conducted over varying substrates (gravel, sand, and black fabric). Deepwater sculpin showed a significant preference for gravel over sand and black fabric. In the absence of siscowet, sculpin movement frequency increased as light intensity decreased. Sculpin reaction distance to siscowet was influenced by both light and substrate. Reaction distance was shortest at low light intensities, peaked at intermediate light intensities (3.05 × 10⁹ to < 6.0 × 10⁹ photons m⁻2 s⁻1), and declined again at the highest light intensities tested. In the presence of siscowet, sculpin activity was suppressed at the upper end of the light range (≥ 6.0 × 10⁹ photons m⁻2 s⁻1). The greatest increase in movement occurred between 6.0 × 10⁹ and 3.05 × 10⁹ photons m⁻2 s⁻1, which corresponded to the range where siscowet prey capture declined, suggesting sculpin exploit this low-light window to move with reduced risk. Reduced activity in the presence of predators is common among cryptic species, and our findings suggest that sculpin restrict movement at higher light levels to avoid detection by siscowet.

Wisconsin↗