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Biodiversity surveys of Wake Atoll—Featuring field guides for plants, arthropods, and herpetofauna

Introduction The U.S. Air Force (USAF) issued funds to the U.S. Geological Survey (USGS) to update the biosecurity plan, create a current (2019) flora and fauna species identification index, and do container evaluations for the presence of potential invasives. The current (2019) biosecurity protocols used for prevention were evaluated, and new biodiversity surveys were completed for terrestrial vegetation and arthropods and included the first formal reptile surveys. Results from field efforts add to existing knowledge and may identify new species arrivals to Wake. One goal of this project was to update and compile established species information for the atoll and create species identification guides for the three taxonomic groups surveyed. We made these flora and fauna species identification guides by compiling results of the recent (2019) and historical surveys. The guides can be used as resident desktop references, as a baseline for assessing future natural resource surveys, and to assist with guiding management actions. We refer herein to biosecurity and integrated pest management plan materials, which we created simultaneously to inform current (2019) biosecurity and to identify some of the top invasive species at Wake. This study was done in cooperation with the USAF, and surveys were performed for the 611th Civil Engineer Squadron Natural Resources Program, ACES PROJECT #YGFZ170002 under agreement number F2MUAA7116GW02 between the USAF and the USGS Western Ecological Research Center.

Open-File Report↗

Updates to CE-QUAL-W2 models for select U.S. Army Corps of Engineers reservoirs in the Willamette Valley Project and an inter-reservoir reach of the Middle Fork Willamette River, northwestern Oregon

Mechanistic models capable of simulating hydrodynamics and water temperature in rivers and reservoirs are valuable tools for investigating thermal conditions and their relation to dam operations and streamflow in river basins where upstream water storage and management decisions have an important influence on river reaches with threatened fish populations. In particular, models allow managers to investigate how new, untried operations or hypothetical structures might influence streamflow and temperature conditions downstream. CE-QUAL-W2 is a two-dimensional (laterally averaged) hydrodynamic water-quality model that has previously been used to investigate the downstream effects of dam operations and other anthropogenic influences on stream temperature in the Willamette River Basin in northwestern Oregon, a region with two populations of fish species designated as threatened under the Endangered Species Act. By linking CE-QUAL-W2 river models to models of upstream, large Willamette Valley Project dams and reservoirs, these models can be used to investigate how dam operations at individual dams can influence streamflow and thermal conditions in downstream river reaches as an integrated system. Integrated model simulations that include the large dams and reservoirs linked to downstream river reaches can help managers develop a better understanding of tradeoffs associated with potential retrofits or operational changes across the multipurpose dams in the Willamette Valley Project, the effect of dam management on downstream tributaries and the Willamette River, and the resulting potential effect on threatened fish populations and habitat conditions. River models capable of simulating river corridors downstream from U.S. Army Corps of Engineers dams were previously updated and integrated to simulate conditions that occurred from March through October of 2011 (a cool and wet year), 2015 (a hot and dry year), and 2016 (a moderately hot and dry year) using CE-QUAL-W2 version 4.2. These river models encompass the following: Coast Fork Willamette and Middle Fork Willamette Rivers, the Row River, and Fall Creek downstream from Cottage Grove, Dexter, Dorena, and Fall Creek Dams, respectively; South Fork McKenzie River downstream from Cougar Dam; McKenzie River downstream from its confluence with the South Fork McKenzie River; South Santiam River downstream from Foster Dam; North Santiam River downstream from Big Cliff Dam; and Willamette River from its start at the confluence of the Middle Fork Willamette and Coast Fork Willamette Rivers to Willamette Falls (river mile 26.0; near West Linn, Oregon). This report documents model modifications, boundary condition data sources or estimation methods, and goodness-of-fit statistics for six CE-QUAL-W2 reservoir models and one river model upstream from the existing river models. These models simulate (1) Hills Creek Lake; (2) Lookout Point Lake and Dexter Reservoir on the Middle Fork Willamette River; (3) the Middle Fork Willamette River reach between Hills Creek Dam upstream and Lookout Point Lake downstream; (4) Cougar Reservoir on the South Fork McKenzie River; (5) Green Peter Lake on the Middle Santiam River and Foster Lake on the South Santiam River; and (6) Detroit Lake and (7) Big Cliff Reservoir on the North Santiam River. These CE-QUAL-W2 models were built by a variety of researchers to simulate a range of conditions in past years; this report documents their upgrade to U.S. Geological Survey (USGS) edition 7 of version 4.2 of CE-QUAL-W2 and updates each model to simulate conditions from January through December of 2011, 2015, and 2016. Also included in this report is an explanation of modifications to the CE-QUAL-W2 source code that constitute USGS edition 7 of CE-QUAL-W2 version 4.2. Each of the models described in this report can be run in isolation or linked to downstream models as a “system model” to simulate conditions in tributaries and (or) in the Willamette Valley Project as a whole. As part of the model updates described in this report, some model parameters were adjusted to improve stability or decrease model error, and boundary conditions including meteorological, hydrologic, and temperature inputs were developed and updated for model years 2011, 2015, and 2016, as necessary. In some cases, the data sources used to drive previous model versions were no longer available, which required the development and checking of new data sources or estimation techniques. Goodness-of-fit statistics for outflow from the dams and in simulated river reaches generally show a good model fit, with the models simulating subdaily water temperatures at most comparable locations with a mean absolute error of generally less than 1 degree Celsius (°C) and a reasonably low bias. Model simulation of the thermal vertical profiles in each reservoir also produced an overall mean absolute error of generally less than 1 °C for all 3 years, with the exception of the Hills Creek Lake Model and the Cougar Reservoir Model in years when the reservoirs did not fill (2015 and 2016). Both of these models have known calibration issues and tend to be sensitive to the choice of certain structural parameters in the model. Overall, the calibration process was focused on obtaining model settings that led to realistic water temperature predictions in all 3 years (2011, 2015, and 2016) without over-calibrating specifically to any single year. A complete investigation of model error for these reservoir submodels was beyond the scope of this investigation but could be undertaken in the future if better model performance for these two reservoirs is desired.

Oregon↗

Results of a modeling workshop concerning preservation and protection of wetlands in North Dakota

In a recently signed letter, the Governor of North Dakota and the Assistant Secretary of the Interior for Fish and Wildlife and Parks charged a joint state-federal study group with examination of two separate questions: 1) mitigation for the Garrison Diversion Project; and 2) planning for long-range protection and preservation of fish and wildlife habitat in North Dakota. The cochair for this study group (the Secretary of the Interior's Field Representative, Denver, Colorado, and the Natural Resources Coordinator for North Dakota) further articulated the charge concerning the second of these two questions to include three steps: 1) development of a general plan for preservation and protection of migratory waterfowl and their associated wetland habitat; 2) a comprehensive analysis of alternative strategies, including opportunities and constraints, for achieving the goals articulated in Step 1; and 3) design of a coordinated state-federal public information program to assist in plan implementation. In order to obtain input from a variety of interests, the joint study group initiated step 2 activities with a five-day workshop in Bismarck, N. D.; December 8-12, 1980. The objectives of the workshop were: 1) to identify alternative strategies for preserving and enhancing waterfowl production habitat in North Dakota; 2) to identify opportunities and constraints associated with those alternatives; and 3) to promote communication and understanding of the implications of those alternatives for all affected parties. To achieve these objectives, the workshop utilized a group of concepts and techniques collectively known as Adaptive Environmental Assessment (AEA). Developed by Dr. C. S. Holling and his co-workers at the University of British Columbia, the AEA process involves planners, managers, scientists, and other interested parties in a structures atmosphere whose focus is the construction and examination of a computerized simulation model of the resource system under consideration. The modeling process is used to promote communication, identify pertinent issues, identify key data gaps and uncertainties, direct research efforts to fill those gaps, and explore the possible consequences of various management alternatives. The workshop, which was facilitated by the AEA Group of the U.S. Fish and Wildlife Service (FWS), was attended by approximately 25 invited participants representing a variety of interests concerned with the wetlands protection issue in North Dakota. During the week workshop participants conceptualized and constructed a computerized simulation model incorporating many of the hydrologic, agricultural, and wildlife aspects of the wetlands issue. During the process of constructing this model and examining its behavior, participants identified several interesting alternative strategies that may prove useful in an overall wetland protection program, along with a variety of constraints associated with each. Perhaps the most interesting of these alternatives revolve around the idea that there may be a variety of cases in which water can be retained on the land, with concommitant benefits both for wildlife and flood control, without detriment to agricultural productivity. Examples of this kind of activity include flooding of previously drained Type I wetlands in summer fallow areas, installation of smaller drains in Type I and III wetlands to reduce the rate at which water runs off in the spring, and use of strategically located gates in drainage channels associated with the state highway system to slow runoff and create wetland habitat. Several other alternatives discussed at the workshop are related to the notion of using available, uncommitted water supplied to enhance or create wetlands. Several cases were cited in which more certain water supplies would be useful in increasing waterfowl production or reducing disease problems, especially in dry years. Water for such purposes might come from a variety of current of proposed water development projects, both large and small scale. Finally, the potential for re-establishment of "unsuccessfully" drained (i.e., not consistently usable for agricultural purposes) wetlands was discussed at some length. There are apparently substantial acreages of such wetlands in North Dakota and a program to acquire and rehabilitate them might be of considerable utility. The workshop was thus successful in accomplishing its first two objectives--identification of alternative strategies, opportunities, and constraints. However, it would be naive to suppose that any of the alternatives discussed offers a complete, simple solution to the wetlands issue in North Dakota. The most important result of the workshop may therefore be that which was accomplished relative to the third objective--promotion of communication and understanding. It was gratifying and encouraging to see the spirit of communication and cooperation that developed by the end of the workshop. The fact that representatives of many of the interests concerned with the wetlands issue participated in an open exchange of ideas and information marks an important step forward. We believe that it is imperative that this cooperative attitude be maintained, and that there are a variety of ways in which this might be accomplished. Perhaps the simplest would be a small-scale pilot project and research effort to determine the effects of wetland maintenance on summer fallow areas. Such a research program would provide not only useful information, but an opportunity for many of the affected interests to begin working toward mutually acceptable solutions to the overall wetlands issue.

North Dakota↗

Upper Mississippi River Restoration future hydrology meeting series

The Upper Mississippi River Restoration (UMRR) program, a broad partnership of State and Federal agencies administered by the U.S. Army Corps of Engineers, integrates ecosystem monitoring, research, and modeling to rehabilitate habitat and evaluate ecosystem trends over time in the Upper Mississippi River System. Hydrologic data are integral to the UMRR program because they are used in scientific research, decision-making, and restoration project planning. However, a lack of quantitative hydrologic data representing potential future conditions limits the ability to complete informative research on how future conditions may affect river ecology, achieve management goals, and design restoration projects for 50-year horizons. The U.S. Geological Survey and the U.S. Army Corps of Engineers led a series of workshops with UMRR partners to (1) prioritize needs for understanding future hydrology, (2) discuss appropriate datasets that could address these needs, and (3) develop a plan for acquiring and distributing a hydrologic dataset of potential future conditions. Agency priorities for understanding future hydrology were broad, spanning ecologic, geomorphic, resource management, and engineering disciplines, and were identified for a range of spatial (project site, navigation pool, reach, system) and temporal (daily, seasonal, annual) scales. The LOcalized Constructed Analogs-Variable Infiltration Capacity-mizuRoute hydrologic data products were identified as a potential source of off-the-shelf data to meet UMRR priority needs but warranted a robust quantitative evaluation. The final meeting in the series scoped a proposal to evaluate the LOcalized Constructed Analogs-Variable Infiltration Capacity-mizuRoute hydrologic data products for use in UMRR applications, including contingencies if the data were determined to be unreliable.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

Void-Filled SRTM Digital Elevation Model of Afghanistan

EXPLANATION The purpose of this data set is to provide a single consistent elevation model to be used for national scale mapping, GIS, remote sensing applications, and natural resource assessments for Afghanistan's reconstruction. For 11 days in February of 2000, the National Aeronautics and Space Administration (NASA), the National Geospatial-Intelligence Agency ian Space Agency (ASI) flew X-band and C-band radar interferometry onboard the Space Shuttle Endeavor. The mission covered the Earth between 60?N and 57?S and will provide interferometric digital elevation models (DEMs) of approximately 80% of the Earth's land mass when processing is complete. The radar-pointing angle was approximately 55? at scene center. Ascending and descending orbital passes generated multiple interferometric data scenes for nearly all areas. Up to eight passes of data were merged to form the final processed Shuttle Radar Topography Mission (SRTM) DEMs. The effect of merging scenes averages elevation values recorded in coincident scenes and reduces, but does not completely eliminate, the amount of area with layover and terrain shadow effects. The most significant form of data processing for the Afghanistan DEM was gap-filling areas where the SRTM data contained a data void. These void areas are as a result of radar shadow, layover, standing water, and other effects of terrain as well as technical radar interferometry phase unwrapping issues. To fill these gaps, topographic contours were digitized from 1:200,000 - scale Soviet General Staff Topographic Maps which date from the middle to late 1980's. Digital contours were gridded to form elevation models for void areas and subsequently were merged with the SRTM data through GIS and image processing techniques. The data contained in this publication includes SRTM DEM quadrangles projected and clipped in geographic coordinates for the entire country. An index of all available SRTM DEM quadrangles is displayed here: Index_Geo_DD.pdf. Also included are quadrangles projected into their appropriate Universal Transverse Mercator (UTM) projection. The country of Afghanistan spans three UTM Zones: Zone 41, Zone 42, and Zone 43. Maps are stored in their respective UTM Zone projection. Indexes of all available SRTM DEM quadrangles in their respective UTM zone are displayed here: Index_UTM_Z41.pdf, Index_UTM_Z42.pdf, Index_UTM_Z43.pdf.

Data Series↗

Demography and behavior of polar bears summering on land in Alaska

Polar bears (Ursus maritimus) in the southern Beaufort Sea population (SB) are spending increased time on the coastal North Slope of Alaska between July and October (Gleason and Rode 2010). The duration spent on land by polar bears, satellite collared on the sea-ice in the spring, during the summer and fall has also increased (USGS, unpublished data; Figure 1). This change in polar bear ecology has relevance for human-bear interactions, subsistence harvest, prevalence of defense kills, and disturbance associated with existing land-based development [e.g., National Petroleum Reserve of Alaska (NPRA), Arctic National Wildlife Refuge (ANWR)], Native Alaskan communities, recreation (ANWR) and tourism (e.g., bear viewing in Kaktovik, AK). These activities have the potential to impact, in new ways, the status of the entire SB population. Concomitantly, the change in polar bear ecology will impact these human activities, and a base-line characterization of this phenomenon can better inform mitigation (e.g., industry permitting under the Endangered Species Act and Marine Mammal Protection Act). In this study we aim to characterize the demography, habitat-use, and aspects of foraging ecology and health of polar bears spending fall on land. The SB population is characterized by a divergent-sea ice ecology, where polar bears typically spend most of the year on the sea-ice, even as the pack ice retreats northward, away from the coast, to its minimal extent in September (Amstrup et al. 2008; Durner et al. 2009). From 2000 – 2005, using coastal aerial surveys, Schliebe et al. (2008) observed between 3.7 and 8% of polar bears from SB (~ 60 – 120 of 1526, Regher et al. 2006) on land during the autumn. Sighting probability was not estimated in these surveys, and therefore the numbers represent minimum numbers of bears on land. Our analysis of USGS data suggest an annual average of 15% (± 3%, SE) of polar bears satellite-tagged on the spring-time sea ice (total n = 18 of 124 satellite tags, 2003 – 2009) come to land during July – October. Based on these data, and an assumption that bears satellite-tagged on the spring time sea ice are representative of the entire SB population of independent bears, there would be an average of 230 bears on land each fall. In contrast to the SB population, in five of the world’s 19 polar bear populations (Obbard et al. 2010), polar bears spend significant periods of time on land (1 – 5 months) when ice completely melts. In these seasonal-ice populations (Amstrup et al. 2008), polar bears are largely in a hypophagic condition (e.g., Hobson et al. 2009), relying on fat stores from the spring hyperphagic season, when ringed seals (Phoca hispida) pup. In general, these seasonal-ice populations are demographically productive (Taylor et al. 2005), although recently an increase in the ice-free season has resulted in a population decline in western Hudson Bay (Stirling et al. 1999; Regehr et al. 2007). There have been measured declines in the body condition and productivity of polar bears in SB, and changes in these parameters have been linked to declining optimal ice habitat (e.g., Durner et al. 2009; Regehr et al. 2010). We do not understand the relationship between land-use and the overall status of the population. Individual polar bears that use land may have increased or decreased fitness, in comparison to polar bears that remain on ice in the autumn. This project, which focuses on the biology of animals that spend time on-shore, will help address this question. This project is funded by the Bureau of Ocean Energy Management (BOEM) under Agreement No. M09PG00025 and the USGS Outer Continental Shelf Program (OCS) for FY 2009-2014. Parts of this study are also funded by US Fish and Wildlife Service, Office of Marine Mammals Management; the Bureau of Land Management; and the North Slope Borough, Department of Wildlife Management. This report is comprehensive, describing results for achieving the overlap

Beaufort Sea, Chukchi Sea↗

Pen rearing and imprinting of fall Chinook salmon. Annual report 1989

The goal of this project is to compare net-pen rearing methods to traditional hatchery methods of rearing upriver bright fall chinook salmon (Oncorhvnchus tshawvtscha). Fish were reared at several densities in net pens at three Columbia River backwater sites during 1984-1987, and in a barrier net at one site during 1984-1986; methods included both fed and unfed treatments. The purpose of this report is to summarize the results obtained from the unfed treatments and the current return of adults from all fed treatments and the barrier net. Zooplankton were the primary food item of unfed fish. Fish reared in net pens utilized insects colonizing the nets as an additional food source, whereas those reared in the barrier net did not. Growth and production of fish reared in the unfed treatments were low. Instantaneous growth rates of unfed fish were much lower than those of the fed treatments and hatchery controls except when zooplankton densities were high and chironomid larvae were important in the diet of unfed fish reared in pens. Only fish in the barrier net treatment resulted in consistent net gains in growth and production over the rearing periods. Adult returns of fish from all fed and unfed treatments are lower than those of control fish reared at the hatchery. Returns appear to be inversely related to rearing density. Even though adult returns are lower than those of traditional hatchery methods, a cost-benefit analysis, as return data becomes more complete, may prove these methods to be an economical means of expanding current hatchery production, particularly if "thinning" releases were used.

Report↗

User's Guide for the MapImage Reprojection Software Package, Version 1.01

Scientists routinely accomplish small-scale geospatial modeling in the raster domain, using high-resolution datasets (such as 30-m data) for large parts of continents and low-resolution to high-resolution datasets for the entire globe. Recently, Usery and others (2003a) expanded on the previously limited empirical work with real geographic data by compiling and tabulating the accuracy of categorical areas in projected raster datasets of global extent. Geographers and applications programmers at the U.S. Geological Survey's (USGS) Mid-Continent Mapping Center (MCMC) undertook an effort to expand and evolve an internal USGS software package, MapImage, or mapimg, for raster map projection transformation (Usery and others, 2003a). Daniel R. Steinwand of Science Applications International Corporation, Earth Resources Observation Systems Data Center in Sioux Falls, S. Dak., originally developed mapimg for the USGS, basing it on the USGS's General Cartographic Transformation Package (GCTP). It operated as a command line program on the Unix operating system. Through efforts at MCMC, and in coordination with Mr. Steinwand, this program has been transformed from an application based on a command line into a software package based on a graphic user interface for Windows, Linux, and Unix machines. Usery and others (2003b) pointed out that many commercial software packages do not use exact projection equations and that even when exact projection equations are used, the software often results in error and sometimes does not complete the transformation for specific projections, at specific resampling resolutions, and for specific singularities. Direct implementation of point-to-point transformation with appropriate functions yields the variety of projections available in these software packages, but implementation with data other than points requires specific adaptation of the equations or prior preparation of the data to allow the transformation to succeed. Additional constraints apply to global raster data. It appears that some packages use the USGS's GCTP or similar point transformations without adaptation to the specific characteristics of raster data (Usery and others, 2003b). It is most common for programs to compute transformations of raster data in an inverse fashion. Such mapping can result in an erroneous position and replicate data or create pixels not in the original space. As Usery and others (2003a) indicated, mapimg performs a corresponding forward transformation to ensure the same location results from both methods. The primary benefit of this function is to mask cells outside the domain. MapImage 1.01 is now on the Web. You can download the User's Guide, source, and binaries from the following site: http://mcmcweb.er.usgs.gov/carto_research/projection/acc_proj_data.html

Open-File Report↗

Multilevel groundwater monitoring of hydraulic head and temperature in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2011-13

From 2011 to 2013, the U.S. Geological Survey’s Idaho National Laboratory (INL) Project Office, in cooperation with the U.S. Department of Energy, collected depth-discrete measurements of fluid pressure and temperature in 11 boreholes located in the eastern Snake River Plain aquifer. Each borehole was instrumented with a multilevel monitoring system (MLMS) consisting of a series of valved measurement ports, packer bladders, casing segments, and couplers. Multilevel monitoring at the INL has been ongoing since 2006 and this report summarizes data collected from 2011 to 2013 in 11 multilevel monitoring wells. Hydraulic head (head) and groundwater temperature data were collected from 11 multilevel monitoring wells, including 177 hydraulically isolated depth intervals from 448.0 to 1,377.6 feet below land surface. One port (port 3) within borehole USGS 134 was not monitored because of a valve failure. Head and temperature profiles reveal unique patterns for vertical examination of the aquifer’s complex basalt and sediment stratigraphy, proximity to aquifer recharge and discharge, and groundwater flow. These features contribute to some of the localized variability even though the general profile shape remained consistent over the period of record. Twenty-two major head inflections were described for 9 of 11 MLMS boreholes and almost always coincided with low‑permeability sediment layers and occasionally thick layers of dense basalt. However, the presence of a sediment layer or dense basalt layer was insufficient for identifying the location of a major head change within a borehole without knowing the true areal extent and relative transmissivity of the lithologic unit. Temperature profiles for boreholes completed within the Big Lost Trough indicate linear conductive trends; whereas, temperature profiles for boreholes completed within volcanic rift zones and near the southern boundary of the Idaho National Laboratory, indicate mostly convective heat transfer. Select boreholes along the southern boundary show a temperature reversal and cooler water deeper in the aquifer resulting from the vertical movement of groundwater. Vertical head and temperature change were quantified for each of the 11 multilevel monitoring systems. Vertical head gradients defined for the major inflections in the head profiles were as high as 2.9 feet per foot. In general, fractured basalt zones displayed relatively small vertical head differences and show a high occurrence within volcanic rift zones. Poor connectivity between fractures and higher vertical gradients were generally attributed to sediment layers and layers of dense basalt, or both. Groundwater temperatures in all boreholes ranged from 10.8 to 16.3 °C. Normalized mean head values were analyzed for all 11 multilevel monitoring wells for the period of record (2007–13). The mean head values suggest a moderately positive correlation among all boreholes and generally reflect regional fluctuations in water levels in response to seasonal climatic changes. Boreholes within volcanic rift zones and near the southern boundary (USGS 103, USGS 105, USGS 108, USGS 132, USGS 135, USGS 137A) display a temporal correlation that is strongly positive. Boreholes in the Big Lost Trough display some variations in temporal correlations that may result from proximity to the mountain front to the northwest and episodic flow in the Big Lost River drainage system. For example, during June 2012, boreholes MIDDLE 2050A and MIDDLE 2051 showed head buildup within the upper zones when compared to the June 2010 profile event, which correlates to years when surface water was reported for the Big Lost River several months preceding the measurement period. With the exception of borehole USGS 134, temporal correlation between MLMS wells completed within the Big Lost Trough is generally positive. Temporal correlation for borehole USGS 134 shows the least agreement with other MLMS boreholes located within the Big Lost Trough; however, borehole USGS 134 is close to the mountain front where tributary valley subsurface inflow is suspected.

Idaho↗

Understanding and forecasting potential recruitment of Lake Michigan fishes by modeling growth and survival of larval stages with coupled climate, biophysical, and bioenergetics models

Individual adult fish can produce huge numbers of small offspring, but most die in the first weeks of life. Environmental changes that lead to even small changes in early life survival can have a disproportionate impact on the number of fish that survive and ultimately support fisheries. Lake Michigan supports valuable recreational and commercial fisheries that can fluctuate with how well fish survive in early life. Statistical models have revealed linkages between survival and climate characteristics, such as water temperature, but the exact mechanisms remain unclear and how future climate will affect the survival of young fish is highly uncertain. We integrated a series of models to investigate how climate variability may explain historical variation in the survival of young alewife and yellow perch, two fish populations that support key fisheries either directly or indirectly, while also projecting their future survival in the mid-21st century under different scenarios informed by consultation with fishery managers. Our model results revealed how spring and summer water temperatures in Lake Michigan can affect the environment in which young alewife and yellow perch grow and survive. Specifically, in years when lake warming is rapid, young fish are more likely to be transported from their natal, productive, nearshore environments to cooler and less productive offshore environments, unless adults also spawn earlier in these warm years. Furthermore, model predictions of prey abundance for young fish in the mid-21st century indicate less favorable conditions for growth and survival compared to predictions based solely on warming temperatures. With completion of the final products in the coming year, including predicted growth and survival of young fish under different future scenarios, fishery managers will have more information to share with stakeholders regarding how expectations may need to be modified regarding alewife and yellow perch productivity.

Lake Michigan↗

Upstream movements of Atlantic Salmon in the Lower Penobscot River, Maine following two dam removals and fish passage modifications

The Penobscot River Restoration Project (PRRP), to be completed in 2016, involved an extensive plan of dam removal, increases in hydroelectric capacity, and fish passage modifications to increase habitat access for diadromous species. As part of the PRRP, Great Works and Veazie dams were removed, making Milford Dam the first impediment to federally endangered Atlantic Salmon Salmo salar . Upstream habitat access for Atlantic Salmon is dependent upon successful and timely passage at Milford Dam because nearly all suitable spawning habitat is located upstream. In 2014 and 2015, a total of 73 adult salmon were radio-tagged to track their upstream movements through the Penobscot River to assess potential delays at (1) the dam remnants, (2) the confluence of the Stillwater Branch and the main stem of the Penobscot River below the impassable Orono Dam, and (3) the Milford Dam fish lift (installed in 2014). Movement rates through the dam remnants and the Stillwater confluence were comparable to open river reaches. Passage efficiency of the fish lift was high in both years (95% and 100%). However, fish experienced long delays at Milford Dam, with approximately one-third of fish taking more than a week to pass in each year, well below the Federal Energy Regulatory Commission passage standard of 95% within 48 h. Telemetry indicates most fish locate the fishway entrance within 5 h of arrival and were observed at the entrance at all hours of the day. These data indicate that overall transit times through the lower river were comparable to reported movement rates prior to changes to the Penobscot River due to the substantial delays seen at Milford Dam. The results of this study show that while adult Atlantic Salmon locate the new fish lift entrance quickly, passage of these fish was significantly delayed under 2014–2015 operations.

Maine↗

Phase 1 studies summary of major findings of the South Bay Salt Pond Restoration Project, South San Francisco Bay, California

Executive Summary The South Bay Salt Pond Restoration Project (Project) is one of the largest restoration efforts in the United States. It is located in South San Francisco Bay of California. It is unique not only for its size—more than 15,000 acres—but also for its location adjacent to one of the nation’s largest urban areas, home to more than 4 million people (Alameda, Santa Clara, and San Mateo Counties). The Project is intended to restore and enhance wetlands in South San Francisco Bay while providing for flood management, wildlife-oriented public access, and recreation. Restoration goals of the project are to provide a mosaic of saltmarsh habitat to benefit marsh species and managed ponds to benefit waterbirds, throughout 3 complexes and 54 former salt ponds. Although much is known about the project area, significant uncertainties remain with a project of this geographic and temporal scale of an estimated 50 years to complete the restoration. For example, in order to convert anywhere from 50 to 90 percent of the existing managed ponds to saltmarsh habitat, conservation managers first enhance the habitat of managed ponds in order to increase use by waterbirds, and provide migratory, wintering, and nesting habitat for more than 90 species of waterbirds. Project managers have concluded that the best way to address these uncertainties is to carefully implement the project in phases and learn from the outcome of each phase. The Adaptive Management Plan (AMP) identifies specific restoration targets for multiple aspects of the Project and defines triggers that would necessitate some type of management action if a particular aspect is trending negatively. U.S. Geological Survey (USGS) biologist Laura Valoppi served as the project Lead Scientist and oversaw implementation of the AMP in coordination with other members of the Project Management Team (PMT), comprised of representatives from the California State Coastal Conservancy, California Department of Fish and Wildlife, the Santa Clara Valley Water District, the U.S. Army Corps of Engineers, and the U.S. Fish and Wildlife Service. To implement the AMP, the PMT have selected and funded applied studies and monitoring projects to address key uncertainties. This information is used by the PMT to make decisions about current management of the project area and future restoration actions in order to meet project. This document summarizes the major scientific findings from studies conducted from 2009 to 2016, as part of the science program that was conducted in conjunction with Phase 1 restoration and management actions. Additionally, this report summarizes the management response to the study results under the guidance of the AMP framework and provides a list of suggested studies to be conducted in “Phase 2–A scorecard summarizing the Project’s progress toward meeting the AMP goals for a range of Project objectives.” The scoring to date indicates that the Project is meeting or exceeding expectations for sediment accretion and western snowy plover ( Charadrius alexandrinus nivosus ) recovery. There is uncertainty with respect to objectives for California gulls ( Larus californicus ), California least tern ( Sternula antillarum ), steelhead trout ( Oncorhynchus mykiss ), and regulatory water quality objectives. Water quality and algal blooms, specifically of the managed ponds, is indicated as trending negative. However, the vast majority of objectives are trending positive, including increased abundance for a number of bird guilds, increasing marsh habitat, maintenance of mudflats, visitor experience, estuarine fish numbers, and special-status marsh species numbers.

California↗

Investigation of otolith microstructure and composition for identification of rearing strategies and associated Baker Lake sockeye salmon (Oncorhynchus nerka) smolt production, Washington, 2016–17

Baker River (Washington, USA) sockeye salmon (Oncorhynchus nerka) are a recovering Puget Sound stock that are aided by trap-and-haul and hatchery programs to mitigate for the presence of a high head dam. The relative contribution of hatchery and natural adults to overall production of smolts and recruits is unknown. The ability to identify three different sockeye production groups (natural production, artificial incubation, and artificial spawning beach) within the Baker system is crucial to moving forward with management goals. The examination of otoliths was proposed as a technical tool for improved understanding and management of Baker sockeye rebuilding efforts. Otoliths were chosen as they provide a chronological record on an individual fish basis and have been shown to identify fish origin through both otolith microstructure and chemistry. The goal of this pilot project was to determine the feasibility of assigning sockeye to their production source based on otolith analysis. A variety of methods were employed and compared for accuracy of group assignment. The maximum overall accuracy capable of attainment was 88.57 percent, however complete confidence (100 percent) in the separation of natural production from artificial production was reached through the analysis of trace elements alone. Some segregation of the two artificial production groups was reached through analysis of a few specific trace elements (magnesium, manganese, and zinc). This confidence in assignment for the artificial production groups was aided by a two-step process of combining trace elements with microstructure. The Sr isotope ratios supported the trace element findings but did not help to boost the overall level of confidence in the separation of production groups. Based upon the results from this preliminary investigation, one could choose a statistically sound, efficient, and cost-effective use of otoliths as a tool for discriminating between the sockeye production groups of the Baker Lake system.

Washington↗

Jurassic magmatism in Dronning Maud Land: synthesis of results of the MAMOG project

The Jurassic Karoo large igneous province (LIP) of Antarctica, and its conjugate margin in southern Africa, is critical for investigating important questions about the relationship of basaltic LIPs to mantle plumes. Detailed aerogeophysical, structural, anisotropy of magnetic susceptibility (AMS), geochronological and geochemical investigations completed under the British Antarctic Survey’s MAMOG project have provided some of the answers. Across most of the area, magma volumes were small compared to those in southern Africa. Jurassic dikes intruding the Archean craton are sparse and the Jutulstraumen trough, a Jurassic rift, is interpreted, from aerogeophysical data, as largely amagmatic. The largest volumes of magma were emplaced along the margin of the craton and close to the Africa-Antarctica rift. Although dikes were emplaced by both vertical and horizontal flow, overwhelmingly magmas in Dronning Maud Land were locally derived, and not emplaced laterally from distant sources. Basaltic magmatism was protracted in Dronning Maud Land (several dike emplacement episodes between ~206 and 175 Ma), and the small magma volumes resulted in highly diverse magma compositions, including picrites and ferropicrites interpreted to have been derived from hot mantle in a mantle plume. The protracted magmatism before the locally ~177 Ma flood lava eruptions, and evidence for a radiating dike swarm, favor a model of mantle plume incubation for 20-30 million years before flood lava eruption.

Open-File Report↗

Non-native fish control below Glen Canyon Dam - Report from a structured decision-making project

This report describes the results of a structured decision-making project by the U.S. Geological Survey to provide substantive input to the Bureau of Reclamation (Reclamation) for use in the preparation of an Environmental Assessment concerning control of non-native fish below Glen Canyon Dam. A forum was created to allow the diverse cooperating agencies and Tribes to discuss, expand, and articulate their respective values; to develop and evaluate a broad set of potential control alternatives using the best available science; and to define individual preferences of each group on how to manage the inherent trade-offs in this non-native fish control problem. This project consisted of two face-to-face workshops, held in Mesa, Arizona, October 18-20 and November 8-10, 2010. At the first workshop, a diverse set of objectives was discussed, which represented the range of concerns of those agencies and Tribes present. A set of non-native fish control alternatives ('hybrid portfolios') was also developed. Over the 2-week period between the two workshops, four assessment teams worked to evaluate the control alternatives against the array of objectives. At the second workshop, the results of the assessment teams were presented. Multi-criteria decision analysis methods were used to examine the trade-offs inherent in the problem, and allowed the participating agencies and Tribes to express their individual judgments about how those trade-offs should best be managed in Reclamation`s selection of a preferred alternative. A broad array of objectives was identified and defined, and an effort was made to understand how these objectives are likely to be achieved by a variety of strategies. In general, the objectives reflected desired future conditions over 30 years. A rich set of alternative approaches was developed, and the complex structure of those alternatives was documented. Multi-criteria decision analysis methods allowed the evaluation of those alternatives against the array of objectives, with the values of individual agencies and tribes deliberately preserved. Trout removal strategies aimed at the Paria to Badger Rapid reach (PBR), with a variety of permutations in deference to cultural values, and with backup removal at the Little Colorado River reach (LCR) if necessary, were identified as top-ranking portfolios for all agencies and Tribes. These PBR/LCR removal portfolios outperformed LCR-only removal portfolios, for cultural reasons and for effectiveness - the probability of keeping the humpback chub population above a desired threshold was estimated to be higher under the PBR/LCR portfolios than the LCR-only portfolios. The PBR/LCR removal portfolios also outperformed portfolios based on flow manipulations, primarily because of the effect of sport fishery and wilderness recreation objectives, as well as cultural objectives. The preference for the PBR/LCR removal portfolios was quite robust to variation in the objective weights and to uncertainty about the underlying dynamics, at least over the ranges of uncertainty investigated. Examination of the effect of uncertainty on the recommended outcomes allowed us to complete a 'value of information' analysis. The results of this analysis led to an adaptive strategy that includes three possible long-term management actions (no action; LCR removal; or PBR removal) and seeks to reduce uncertainty about the following two issues: the degree to which rainbow trout limit chub populations, and the effectiveness of PBR removal to reduce trout emigration downstream into Marble and eastern Grand Canyons, where the largest population of humpback chub exist. In the face of uncertainty about the effectiveness of PBR removal, a case might be made for including flow manipulations in an adaptive strategy, but formal analysis of this case was not conducted. The full set of conclusions described above is not definitive, however. This analysis described in this report is a simplified depiction of the t

Open-File Report↗

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↗

Undiscovered oil and gas resources underlying the U.S. portions of the Great Lakes, 2005

The U.S. Geological Survey (USGS) completed an assessment of the undiscovered oil and gas potential of the U.S. portions of the Appalachian Basin and the Michigan Basin in 2002 and 2004, respectively. Following the assessments of these two basins, oil and gas allocations were assigned to the U.S. portions of the Great Lakes - Lake Superior (Michigan, Minnesota, and Wisconsin), Lake Michigan (Illinois, Indiana, Michigan, and Wisconsin), Lake Huron (Michigan), Lake Erie (Michigan, New York, Ohio, and Pennsylvania), and Lake Ontario (New York). Allocations for Lake St. Clair (Michigan) were included with those of Lake Erie. The allocations are based on the geologic elements of each total petroleum system defined in the region and the projected extent of those elements from onshore beneath each of the lakes. These geologic elements include the hydrocarbon source rocks, reservoir rocks, and traps. By using this geologic framework, the USGS defined 8 total petroleum systems and 21 assessment units within the Great Lakes and estimated the quantity of undiscovered technically recoverable oil and gas resources within 16 of the 21 assessment units in the Great Lakes.

Fact Sheet↗

Ground-water contamination by crude oil at the Bemidji, Minnesota, research site- An introduction: Chapter A in Ground-water contamination by crude oil at the Bemidji, Minnesota, research site; US Geological Survey Toxic Waste--ground-water contamination study

The U.S. Geological Survey has begun a research project to improve understanding of the mobilization, transport, and fate of petroleum contaminants in the shallow subsurface and to use this understanding to develop predictive models of contaminant behavior. The project site is near Bemidji in northern Minnesota where an accidental spill of 10,500 barrels of crude oil occurred when a pipeline broke on August 20, 1979. Regulatory and remedial actions have been completed. The site is in a remote area with neither man-made hydraulic stresses nor other anthropogenic sources of the compounds of interest. The spill is in the recharge area of a local flow system that discharges to a small closed lake approximately 1,000 feet down the hydraulic gradient. The aquifer is pitted outwash dissected by younger glacial channels and is underlain by poorly permeable till at a depth of about 80 feet. Ground water dissolves oil floating on the water table under the spill site and moves toward the lake. At the water table, ground water enters the lake through lacustrine sediments; at depth, flow may be underneath the lake through the outwash. Contaminant transport has been as rapid as 4 feet per day based on the rate of movement of contaminants monitored through wells installed within a few days of the spill, but average rates are undoubtedly much less.

Minnesota↗