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89 records · Page 4Linked to original sources
USGS2026

Assessing the state of hydrologic science in the Upper Klamath Basin—A comprehensive review of data, tools, and models

Water demand in the Upper Klamath Basin (UKB) from various stakeholders and ecological needs often outstrips available supply, leading to persistent management challenges. This study reviews the state of hydrologic science within the UKB as of 2025—specifically, the tools, data, and models available for assessing five key components of the water system: (1) surface water; (2) precipitation; (3) evapotranspiration; (4) groundwater; and (5) water use. The UKB water supply is critical for Native American communities, regional agriculture, and federally listed fishes and faces challenges from competing needs, climate variability, and operational/regulatory requirements. We assess existing datasets, regional and national models, and historical studies to understand the available resources and identify gaps that may hinder integrated water assessments and management. Our findings indicate areas where improvements in data collection and model precision could improve the accuracy of water-availability forecasts and support water-management practices. This review can inform near-term forecasting, assist in optimizing water-resource data collection and management strategies, and support regional water-availability assessments of the basin.

Oregon↗
USGS2026

Recent scientific contributions by the U.S. Geological Survey in the San Francisco Bay and Sacramento–San Joaquin Delta Estuary

Introduction The San Francisco Bay and Sacramento–San Joaquin Delta Estuary (hereafter, Bay-Delta) is the largest estuary on the West Coast of the United States. The Bay-Delta covers more than 1,600 square miles and drains a watershed of more than 75,000 square miles, which is greater than 40 percent of California. The region surrounding the Bay-Delta is home to about 10 million people, and its habitats (fig. 1) support more than 800 plant and animal species. The waterways of the Bay-Delta are the central hub of California’s extensive freshwater delivery system, supplying water to more than 27 million Californians and 4 million acres of farmland in the Central Valley. The U.S. Geological Survey (USGS) is the primary science agency of the U.S. Department of the Interior, providing a broad range of Earth, water, biological, and mapping data and expertise to inform natural resource management across the country. This fact sheet focuses on research conducted by the USGS in the Bay-Delta region, mostly within the past 5 years. The fact sheet is organized across five major themes: water flow and water quality, fish and wildlife, wetland restoration, invasive species, and hazards. In each of these areas, the USGS works closely with Federal, State, and local agencies; academia; and non-governmental organizations to provide objective, evidence-based science. The data and knowledge gained from USGS research and monitoring are publicly available and are routinely used by agencies, including the U.S. Bureau of Reclamation, U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service, California Department of Water Resources, California Department of Fish and Wildlife, California State Water Resources Control Board, Delta Stewardship Council, and many additional organizations and stakeholders to inform management of the Bay-Delta region and its resources.

California↗
USGS2026

A geographic dataset of rocky reefs habitat areas of particular concern for the United States West Coast

The United States National Marine Fisheries Service determines “essential fish habitat (EFH)” for federally managed species in coordination with regional fishery management councils, considers adverse effects to those habitats, and provides information to further habitat conservation and enhancement. Identifying discrete subsets of EFH as “habitat areas of particular concern (HAPC)” can help focus conservation, management, and research efforts. In 2006, the Pacific Fishery Management Council designated rocky reefs along the United States (U.S.) West Coast as HAPCs for groundfishes because of their ecological significance, sensitivity to human impacts, and relative rarity. To better understand where rocky reefs occur, we (1) located rocky reef areas that were not included in the 2006 rocky reef dataset, and (2) incorporated best available data into a refined geographic dataset that enables visualization. Our update shows that rocky reefs are distributed throughout the U.S. West Coast continental margin, are patchier than previously known, and comprise 8% of the extent of all data inputs. This updated dataset will inform resource management decisions in coastal and marine environments.

California, Oregon, Washington↗
USGS2024

Utility of an instantaneous salt dilution method for measuring streamflow in headwater streams

Streamflow records are biased toward large streams and rivers, yet small headwater streams are often the focus of ecological research in response to climate change. Conventional flow measurement instruments such as acoustic Doppler velocimeters (ADVs) do not perform well during low-flow conditions in small streams, truncating the development of rating curves during critical baseflow conditions dominated by groundwater inflow. We revisited an instantaneous solute tracer injection method as an alternative to ADVs based on paired measurements to compare their precision, efficiency, and feasibility within headwater streams across a range of flow conditions. We show that the precision of discharge measurements using salt dilution by slug injection and ADV methods were comparable overall, but salt dilution was more precise during the lowest flows and required less time to implement. Often, headwater streams were at or below the depth threshold where ADV measurements could even be attempted and transects were complicated by coarse bed material and cobbles. We discuss the methodological benefits and limitations of salt dilution by slug injection and conclude that the method could facilitate a proliferation of streamflow observation across headwater stream networks that are highly undersampled compared to larger streams.

Virginia↗
USGS2026

Keeping pace: Migrating sea lampreys adjust swim speed in response to shifting water velocity to maintain a constant ground speed

Upstream migrating fish must balance energetic costs with environmental and ecological constraints. Theoretical models predict that fish can conserve energy by adjusting swim speed in response to changing water velocity, but detailed field tests of these predictions remain rare. We used fine-scale acoustic telemetry and hydrodynamic modeling to track adult sea lamprey (Petromyzon marinus) migrating through a river and evaluated how movement speeds varied with environmental conditions and individual traits. Swim speed increased with faster water velocities, while ground speed remained constant, supporting the hypothesis that lampreys regulate swim effort to maintain a fixed migration pace. The average ground speed aligned with a predicted optimum of ∼1 body length per second. Both swim and ground speeds declined slightly in deeper water, suggesting a trade-off between movement efficiency and predator avoidance. These findings provide field-based support for a theoretical model of energy optimization and underscore how migratory fish adaptively adjust behavior to local hydrodynamic conditions. Our results highlight the value of using high-resolution tracking and environmental modeling to reveal behavioral tactics that underlie efficient migration strategies.

Michigan↗
USGS2026

Navigating uncertainty and competing objectives: Spring chinook salmon recovery in the upper Willamette river

Globally, anadromous fish populations are threatened with extinction due to multiple factors, including river impoundments that block migration, widespread alteration of physical habitat, temperature, and flow regimes, commercial and recreational harvest, changes in biological communities, and long-term climate trends. In this synthesis, we describe how physical and biological factors, policy and law, and public resource allocation affect management of spring-run Chinook Salmon ( Oncorhynchus tshawytscha ) in the Upper Willamette River (UWR), Oregon, USA. Efforts to restore salmon populations often involve trade-offs, for example, water management decisions must account for flood control, agricultural and municipal water use, and management of other species. UWR Chinook Salmon recovery efforts are also governed by multiple laws, policies, and action agencies that in some cases have incongruent objectives. Competing and conflicting objectives, combined with uncertainty regarding the outcomes of proposed management actions, create significant challenges for decision makers. Resource limitations, regulatory constraints, and incongruent objectives have created challenges for managers in the UWR, but opportunities exist for improved adaptive management and collaboration, which could build trust and engagement among stakeholders and ultimately support the successful implementation of decision tools. A suite of decision support tools that have been used in the Willamette River basin and elsewhere across the range of Pacific salmon have the potential to enhance decision processes. These tools can be effective when decision makers and stakeholders commit to long-term, collaborative utilization of the tools for decision making, and when available resources and regulatory environments are conducive to implementation and adaptive refinement of both the decision-support tools and management plans. The general biological and institutional principles discussed for UWR Chinook Salmon in this work apply more generally to populations of anadromous fishes across their range, especially to populations in highly regulated river systems.

Oregon↗
USGS2025

Mapping potential sensitivity to hydrogeomorphic change in the UMRS riverscape

In 2020 the U.S. Geological Survey (USGS), as part of the Upper Mississippi River Restoration (UMRR) Program, began a new project to characterize potential hydrogeomorphic change associated with hydrogeomorphic units (HGUs) and their catenae (units linked by their association with sediment sources and flow origins). The goal of the project was to develop a geographic information system (GIS) database of HGUs for the Upper Mississippi River System (UMRS) available to both scientists and river managers working on UMRR studies and HREP planning and design studies. The characterization was based on a hydrogeomorphic change hierarchical classification developed previously for the UMRS. The products were generated with automated techniques in a GIS using systemic datasets. Landforms were mapped from the 2015 UMRS topobathymetric dataset with geomorphon (shape-based) tools tailored for the large riverscape, valley bottom environments in the UMRS. A clustering analysis was applied to the resulting landforms to identify HGUs associated with zones of perennial low flows, bankfull flows, and overbank floodplains. Catenae were assembled based on the proximity of the units to the main channel, tributary mouths, and side channels from previously published aquatic areas (USACE, 2018) coupled with least-cost flowpath linkages between potential sediment origins and planform change units developed by Rogala, Fitzpatrick, and Henderson (2020). These GIS-based analyses were successful at identifying a range of HGUs using an automated technique with available data across the entire riverscape, with emphasis on those that have the potential for hydrogeomorphic change. Most of the resulting features are depositional, as expected in a large river system. However, this is the first attempt of linking tributary inputs, side channel erosion and levee breaches with their depositional counterparts. The approach was successfully piloted in Pools 8 and 10 in the Upper Impounded Reach and Pool 14 in the Lower Impounded Reach, with next steps for application in reaches of the unimpounded section and Illinois River. This report emphasizes results from Pool 10, which was the focus of most of our attention during the pilot phase.

Illinois, Indiana, Iowa, Minnesota, Missouri, Sout↗
USGS2024

Groundwater and surface-water interactions in the Lower Duwamish Waterway, Seattle, Washington

The U.S. Geological Survey (USGS), in cooperation with the Washington State Department of Ecology (Ecology), conducted a study to describe the current understanding of the regional groundwater system of the lower Duwamish River valley and groundwater and surface-water interactions in the lower Duwamish Waterway. The lower Duwamish Waterway is the final 5-mile (mi) reach of the Duwamish River before it empties into Elliott Bay in Puget Sound near Seattle, Washington. A nearshore site (hereinafter referred to as “Nearshore Site” to distinguish the particular site from general discussions of nearshore areas) along the western shoreline of the Duwamish River, about 1.5 mi upstream from the river mouth, was selected for focused groundwater data collection by USGS. Data loggers were deployed in seven groundwater wells and one stilling well in the Duwamish River to measure specific conductance, temperature, and depth at 15-minute intervals for a period of about 2 years. At the Nearshore Site during 2020–22, water levels in the shallow wells were 3–8 feet (ft) higher than water levels in the deep wells, providing evidence for a low-permeability layer between the shallow and deep aquifers in this area. The shallow wells had a pronounced seasonal variability, with high water levels in winter and low water levels in summer. Data from the deep wells showed far less seasonal variability, with slight increases in winter and a near-constant water level from spring to autumn. The deep wells had a strong hydraulic connection to the Duwamish River, as evidenced by the synchronous water-level variability during the tidal cycle, whereas the shallow wells had minimal to no tidal response. The potentiometric maps developed for the Nearshore Site and surrounding areas indicate large differences in groundwater-flow directions for the shallow and deep aquifers at low and high tides. For the shallow aquifer, flow is toward the lower Duwamish Waterway near the Nearshore Site, regardless of the tidal condition. For the deep aquifer, a potentiometric trough forms parallel to the shoreline during high tide, indicating that groundwater flow converges from the uplands to the west and the Duwamish River to the east. The geometry of the potentiometric surfaces between the nearshore-most well and the shoreline is complex and is further confounded by intermittent shoreline armoring and other buried infrastructure, which could serve as either a barrier or a conduit to flow. Groundwater and surface-water interactions in the lower Duwamish Waterway are inherently complex as a result of three overarching factors. First, water levels in the lower reaches of the Duwamish River vary daily by 11–16 ft because of tides from Puget Sound, which create large swings in the hydraulic gradient in the nearshore groundwater system. Second, the density and chemical composition of water in the Duwamish River change daily with the tides and seasonally, which constrains how river water entering the nearshore sediments interacts with discharging groundwater. Third, the nearshore subsurface and shoreline conditions are heterogenous because of extensive shoreline armoring over the past century, which governs the flow of groundwater and infiltrating river water. These unique features of groundwater and surface-water interactions in the lower Duwamish Waterway thus govern the transport of terrestrial contaminants to the lower Duwamish Waterway. Furthermore, the heterogenous aquifer properties in the lower Duwamish Waterway contribute to spatially and temporally dynamic contaminant-transport processes.

Washington↗
USGS1998

Ground-water flow in the surficial aquifer system and potential movement of contaminants from selected waste-disposal sites at Cecil Field Naval Air Station, Jacksonville, Florida

As part of the Installation Restoration Program, Cecil Field Naval Air Station, Jacksonville, Florida, is considering remedialaction alternatives to control the possible movement of contaminants from sites that may discharge to the surface. This requires a quantifiable understanding of ground-water flow through the surficial aquifer system and how the system will respond to any future stresses. The geologic units of interest in the study area consist of sediments of Holocene to Miocene age that extend from land surface to the base of the Hawthorn Group. The hydrogeology within the study area was determined from gamma-ray and geologists' logs. Ground-water flow through the surficial aquifer system was simulated with a seven-layer, finite-difference model that extended vertically from the water table to the top of the Upper Floridan aquifer. Results from the calibrated model were based on a long-term recharge rate of 6 inches per year, which fell in the range of 4 to 10 inches per year, estimated using stream hydrograph separation methods. More than 80 percent of ground-water flow circulates within the surficial-sand aquifer, which indicates that most contaminant movement also can be expected to move through the surficial-sand aquifer alone. The surficial-sand aquifer is the uppermost unit of the surficial aquifer system. Particle-tracking results showed that the distances of most flow paths were 1,500 feet or less from a given site to its discharge point. For an assumed effective porosity of 20 percent, typical traveltimes are 40 years or less. At all of the sites investigated, particles released 10 feet below the water table had shorter traveltimes than those released 40 feet below the water table. Traveltimes from contaminated sites to their point of discharge ranged from 2 to 300 years. The contributing areas of the domestic supply wells are not very extensive. The shortest traveltimes for particles to reach the domestic supply wells from their respective contributing areas ranged from 70 to 200 years.

Florida↗
USGS2025

Leveraging wildfire to augment forest management and amplify forest resilience

Successive catastrophic wildfire seasons in western North America have escalated the urgency around reducing fire risk to communities and ecosystems. In historically frequent-fire forests, fuel buildup as a result of fire exclusion is contributing to increased fire severity. The probability of high-severity fire can be reduced by active forest management that reduces fuels, prompting federal and state agencies to commit significant resources to increase the pace and scale of fuel reduction treatments. However, lower severity areas of wildfires also have the potential to act as “treatments,” and even catastrophic fires with large areas of high severity can still have substantial areas of lower severity fire that may be improving forest conditions locally. We quantified active management and wildfire severity across yellow pine and mixed conifer (YPMC) forests in the Sierra Nevada of California over a 22-year period (2001–2022). We did not detect increases in the area treated through time, but the area of beneficial wildfire (low to moderate severity) increased substantially, exceeding active treatment area in 8 of 22 years. Overall, beneficial wildfire treated ~17% more area than all treatments combined, and roughly four times more area than fire-related treatments alone. We then used disturbance history to evaluate resistance to high-severity wildfire and forest loss across the YPMC range. Of the 2.3 million ha YPMC of forests in 2001, 20% lost mature forests due to high-severity fire by 2022, which is nearly half of all YPMC area burned. Most of the landscape (47%) remains at risk of high-severity fire because it had no restorative disturbances, but 33% of the study area has some level of resistance to high-severity wildfire. In these areas, resistance will need to be enhanced and maintained over time via active management or managed wildfire, but these treatment needs will likely outpace capacity even under optimistic implementation scenarios. Given limited resources for implementing active management and the likelihood of a more fiery future, incorporating beneficial wildfire into landscape-level treatment planning has the potential to amplify the impact of active management treatments.

California, Nevada↗
USGS2026

Spatially referenced watershed models for the binational Red–Assiniboine River Basin: Bayesian vs frequentist comparison

Excess nutrient loading remains a leading cause of declining water quality in lakes, estuaries, and coastal waters worldwide, with global economic costs of US$200 billion – US$2 trillion annually from impacts on fisheries, tourism, freshwater resources, and water treatment. Our study focuses on total phosphorus (TP) in Lake Winnipeg and its binational Red-Assiniboine River Basin, where nutrient inputs have degraded water quality and increased cyanobacterial blooms. These changes pose ecological, public health, and economic risks. We applied a spatially referenced watershed model with a hybrid statistical-mechanistic structure partitioning annual nutrient loads into land-use export, land-to-water delivery, and in-reservoir decay. Bayesian and traditional frequentist model calibrations were compared. In the frequentist model, coefficients for agricultural inputs, forests /wetlands, stream channels, precipitation, and reservoir losses were statistically significant, whereas coefficient for wastewater was not. In contrast, all variables were successfully calibrated using the Bayesian approach. Model results delineate TP-export hotspots across the basin, showing that 54–62% of TP originates from the U.S., with agricultural sources ranging 62–72%—highlighting the importance of agriculture-focused Best Management Practices. Given the global relevance of nutrient-driven water-quality challenges, our results highlight Bayesian calibration for robust risk assessment and adaptive nutrient management.

Red–Assiniboine River Basin↗
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↗
USGS2026

Linking distribution and return-on-investment models to optimize woody management for prairie grouse in Nebraska

Grasslands in Nebraska, USA, face threats from agricultural conversion, urban development, and woody encroachment, all of which negatively affect prairie grouse ( Tympanuchus spp.) populations. To optimize conservation planning, Nebraska wildlife agencies developed probabilistic area-based surveys for greater prairie-chicken ( T. cupido ) and sharp-tailed grouse ( T. phasianellus ) to sample landscapes across a range of environmental conditions. This design improves historical surveys and enables the development of distribution models that quantitatively define habitat associations and support scenario-based conservation planning. Using survey data collected during 2020–2022, we modeled prairie grouse occurrence and abundance as functions of land cover, topography, and climate using Bayesian logistic and zero-inflated negative binomial models with regularized horseshoe priors. We then conducted a maximum potential return-on-investment analysis of woody cover treatments, assuming sustained treatment success, relative to projected impacts of woody encroachment on prairie grouse populations by 2050. Among modeled associations were a positive association with grasslands having low woody cover and a negative association with grasslands having high woody cover. Across the 3-year period, median estimated annual populations were 142,380 for greater prairie-chicken (range of 95% CIs across years = 68,821–277,615) and 64,154 for sharp-tailed grouse (range of 95% CIs across years = 27,550–146,559). Under projected woody encroachment, mean predicted population declines were 10% for greater prairie-chicken (range of 95% CIs = 7–14%) and 6% for sharp-tailed grouse (range of 95% CIs = 5–7%). Areas with high prairie grouse density and low treatment costs in 2021, and high projected woody encroachment and population loss by 2050, offered the greatest return on investment for woody management. Return on investment was greatest in the northwestern Shortgrass Prairie ecoregion (northwestern Nebraska) for sharp-tailed grouse and the eastern Sandhills ecoregion (central Nebraska) for both species. These models underscore the value of evidence-based, quantitative approaches for prioritizing conservation actions on working lands. Scenario-based modeling could be extended to guide other treatments, such as optimizing restoration (e.g., Conservation Reserve Program) or incentivizing grassland persistence in areas with predicted climate resilience.

Nebraska↗
USGS2025

Shallow geologic framework of the Mississippi Sound and the potential for sediment resources

The Mississippi Sound, an estuarine environment located between the mainland and barrier islands bordering the northern Gulf of America (formerly the Gulf of Mexico), serves as a vital ecosystem for the States of Mississippi and Alabama. Spanning approximately 100 kilometers from east to west and covering 1,400 square kilometers, the sound is home to marine industry and ports, and its shallow and brackish waters sustain a diverse array of marine life. Barrier islands along the southern edge of the sound separate the microtidal estuary from the Gulf of America. This protection from gulf wave action mediates current flow within the sound, resulting in predominantly fine-grained sediment deposition along the seafloor. This study, conducted by the U.S. Geological Survey in cooperation with the U.S. Army Corps of Engineers, provides insight on fluvial and tidal processes spanning the past 5,000 years. The report synthesizes existing research to provide a comprehensive overview of the sound geology, from Pleistocene origins to present-day morphology, and utilizes high-resolution single channel seismic profiles and sediment data to identify and map sedimentary deposits and morphologic features at and below the seafloor. Despite its ecological significance, the Mississippi Sound faces environmental challenges, including water-quality issues, habitat degradation, storm-induced erosion, and the ongoing threats of sea-level rise and environmental changes. This study uses the present-day understanding of the sound's geology to inform coastal management decisions, hazard assessment, and potential mineral resources.

Louisiana, Mississippi↗
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

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↗