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At least 19 recordsLinked to original sources
USGS2020

2020 Four-band aerial imagery testing and acquisition for 2020 land cover/land use mission

The aerial camera testing project lays the groundwork for the collection of aerial imagery that will be used in the creation of the next iteration of systemic land cover/land use data for the Upper Mississippi River System. Prior to acquisition in the summer of 2020, the new 4-band aerial camera will be assessed for image quality at various resolutions and be compared to the camera used for the 2010/2011 collection. Systemic aerial imagery has been acquired, and vegetation datasets derived from that imagery, by the Upper Mississippi River Restoration Program’s Long Term Resource Monitoring element on a decadal basis beginning in 1989 and follow-up imagery missions in 2000 and 2010/2011. Remote sensing and geographic information system technology has changed dramatically during this time, transitioning from a workflow based on 9-inch by 9-inch aerial film-based cameras to today’s 80-megapixel four-band digital camera. In addition to the camera testing, this report also provides historical information of previous aerial imagery acquisition efforts and how that process has continued to advance in the 30 years since the Program’s genesis.

Long Term Resource Monitoring Technical Report↗
USGS2016

Accuracy assessment/validation methodology and results of 2010–11 land-cover/land-use data for Pools 13, 26, La Grange, and Open River South, Upper Mississippi River System

Introduction/Background The U.S. Geological Survey (USGS)-Upper Midwest Environmental Sciences Center (UMESC) was responsible for development of several land cover/land use (LCU) systemic datasets of the Upper Mississippi River System (UMRS). These efforts (1989 and 2000) were funded by the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration Program (UMRR) Long Term Resource Monitoring (LTRM) element. Development of systemic datasets includes the acquisition, processing, and serving of high-resolution aerial photography and land cover/land use spatial datasets ( http://www.umesc.usgs.gov/data_library/land_cover_use/land_cover_use_data.html ). In 2008, the UMRR reached a collaborative agreement with the U.S. Fish and Wildlife Service-Region 3 to collect high-resolution digital imagery of the entire UMRS floodplain during 2010–11 for LTRM. The UMESC helped acquire, process, and serve this imagery, as well as produce and serve the 2010–11 LCU systemic dataset of the UMRS floodplain. Digital imagery for Pools 13, 26, La Grange, and Open River South was collected using an Applanix DSS 439 digital sensor system with a 40 millimeter lens and Color Infrared (CIR) filter. The imagery was collected at a resolution of 20 centimeters/pixel (8 inches/pixel) for Pool 13 and 40 centimeters/pixel (16 inches/pixel) for Pools 26, Open River South, and La Grange. All imagery was projected to Universal Transverse Mercator (UTM) Zone 15, North American Datum of 1983 (NAD 83). The General Wetland Vegetation Classification (GWVC) system used for mapping is hierarchical, and its 31 classes can be collapsed into broader categories using either a 15- or 7-class level. While the 1989 and 2000 LCU systemic datasets have not gone through a traditional thematic accuracy assessment (AA) in the past, nor have they undergone a validation analysis, the end products are of high quality. For each systemic dataset produced (1989, 2000, 2010–11), extensive field reconnaissance is performed before photointerpretation. The intent of this field reconnaissance is to learn, test, and verify image signatures as they relate to vegetation types. Questionable areas on the imagery are visited, and the plants or land features observed in the area are recorded for reference. This procedure verifies vegetation signatures on the imagery with those on the ground. In addition, once the photointerpretation is complete, the final LCU dataset undergoes extensive quality assurance/quality control to ensure the imagery is mapped correctly. Since the 2000 LCU systemic dataset was developed, there has been a growing interest in completing thematic AAs for the LTRM LCU spatial datasets. The objective of an AA is to measure the probability that a particular location has been assigned its correct vegetation class. An AA estimates thematic (map class) errors in the data, giving users information needed to determine data suitability for a particular application. At the same time, data producers are able to learn more about the nature of errors in the data. Thus, the two attributes of an AA are “producers’ accuracy,” which is the probability that an AA point has been mapped correctly (also referred to as an error of omission); and “users’ accuracy,” which is the probability that the map actually represents what was found on the ground (also referred to as error of commission). Producers’ and users’ accuracies can be obtained from the same set of data by using different analyses. Accuracy assessment is an extensive effort that requires seasonal field personnel and equipment, data entry, analyses, and post processing—tasks that are costly and time consuming. The geospatial team at the UMESC has suggested a validation process for understanding the accuracy of the spatial datasets, which will be tested on at least some areas of the UMRS. Validation is not a true verification of map-class type in the field; however, it can provide the user of the map with useful information that is similar to a field AA. Similar to an AA, validation involves generating random points based on the total area for each map class. However, instead of collecting field data, two or three individuals not involved with the photo-interpretative mapping separately review each of the points onscreen and record a best-fit vegetation type(s) for each site. Once the individual analyses are complete, results are joined together and a comparative analysis is performed. The objective of this initial analysis is to identify areas where the validation results were in agreement (matches) and areas where validation results were in disagreement (mismatches). The two or three individuals then perform an analysis, looking at each mismatched site, and agree upon a final validation class. (If two vegetation types at a specific site appear to be equally prevalent, the validation team is permitted to assign the site two best-fit vegetation types.) Following the validation team’s comparative analysis of vegetation assignments, the data are entered into a database and compared to the mappers’ vegetation assignments. Agreements and disagreements between the map and validation classes are identified, and a contingency table is produced. This document presents the AA processes/results for Pools 13 and La Grange, as well as the validation process/results for Pools 13 and 26 and Open River South.

Iowa, Illinois, Minnesota, Missouri, Wisconsin↗
USGS2016

Documenting the use of the Long Term Resource Monitoring element’s fish monitoring methodologies throughout the Midwest

The Upper Mississippi River Restoration (UMRR) Program’s Long Term Resource Monitoring (LTRM) element is designed to monitor and assess long term trends in the Upper Mississippi River System (UMRS). To accomplish this, standardized methods are used that allow for comparisons across pools and rivers. In recent years, other projects and other agencies have adopted the LTRM fish methodologies for use outside the UMRR. To determine how widespread the use of the Fish Component’s methods are, a twelve question survey was delivered via SurveyMonkey.com through the states comprising the American Fisheries Society (AFS) North Central Division and the Upper Mississippi River Conservation Committee. Approximately 2,000 professionals were reached with ≈11 percent participating. Results indicate that nearly all (95 percent) respondents use standardized methods in their sampling and 48 percent are familiar with the LTRM fish methodologies. Roughly one-third (35 percent) of all respondents have used the methods in the past and most (78 percent) of those have modified the methods to suit the information needs specific to their fishery. Results indicate that the LTRM methods have indeed spread outside the UMRR and are now a well-known and potentially widely used technique to sample fish communities.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗
USGS2019

Scientific Framework for resilience research on the Upper Mississippi River System

The goal of this research framework is to outline research that would continue to improve our understanding of ecological resilience of the Upper Mississippi River System (UMRS) and inform management of the system for health and resilience. We provide a broad overview of recently completed and ongoing work that has been funded as a part of the UMRS Ecological Resilience Assessment and related efforts to provide context for how proposed research questions build upon our current knowledge and may inform restoration planning and design. We describe two primary objectives within this research framework - the first objective is to investigate hypothesized drivers and feedbacks related to specified resilience, and the second is to expand our utility of general resilience indicators through further development and evaluation. The intended audience for this framework is the Upper Mississippi River Restoration Program (UMRR). The UMRR partnership is made up of natural resource agencies from five states (Illinois, Iowa, Minnesota, Missouri and Wisconsin) and five federal agencies (U.S. Army Corps of Engineers, U.S. Environmental Protection Agency, U.S. Fish and Wildlife Service, U.S. Geological Survey, and USDA Natural Resources Conservation Service).

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗
USGS2020

Mapping the thermal landscape of the Upper Mississippi River

Temperature has a fundamental influence on physical, chemical and biological processing in aquatic ecosystems. River temperatures respond to a diverse array of drivers including air temperature, streamflow, and thermal inputs, but the physical template has been shown to play a significant role in structuring spatial and temporal variation in water temperature. How these factors interact to affect water temperature in complex floodplain river habitats such as those present in the Upper Mississippi River System (UMRS) is not well-studied. We used a combination of airborne thermal imagery and continuous temperature loggers deployed across aquatic area types to evaluate spatial and temporal patterns in water temperature in Navigation Pool 8 during the summer and fall of 2017. The mid-wave infrared thermal camera available for this study is not commonly used for thermal imagery acquisition over water, so we discuss accommodations that were made to account for potential interferences and describe considerations for future users interested in using the technology. We quantified thermal metrics from imagery and continuous loggers (e.g., mean, coefficient of variation, range) and compared those to hydrogeomorphic variability across aquatic areas using a Geographic Information System (GIS) dataset. Our findings showed that both temporal and spatial temperature patterns were linked to variation in depth and connectivity of aquatic areas across the pool. Despite some of the technical challenges associated with acquiring this imagery, the method shows promise for characterizing spatial variation in surface temperatures in the UMRS associated with complex physical features such as habitat rehabilitation and enhancement projects.

Iowa, Illinois, Minnesota, Wisconsin↗
USGS2020

Recent planform changes in the Upper Mississippi River

Geomorphic changes in the Upper Mississippi River (UMR) have long been a concern of river agencies charged with maintaining and restoring river habitat (GREAT 1980; Jackson et al. 1981; USFWS 1992). Large meandering alluvial rivers like the UMR are expected to constantly change and adjust their fluvial landforms within their riparian corridors as a result of the natural interaction of hydrologic processes, sediment movement, and vegetation over time. However, present geomorphic changes in the UMR reflect altered hydrologic, hydraulic, and sediment conditions caused by regulated flows, constructed agricultural levees and navigation dams, altered land use in the watershed, and climate change. Levees reduce lateral hydrologic and sediment connectivity between channels and floodplains on many tributaries and on the Mississippi River downstream of Pool 13. Between each of the dams are a repeating series of landforms associated with tailwater, intermediate, and impounded conditions. The dams maintain a minimum water level, thus creating many off-channel areas that act as sediment traps. Whereas high-head dams cut off sedimentological connectivity longitudinally through the river corridor (Skalak et al., 2013), low head dams on the UMR only slightly altered transport longitudinally. Deltaic-like sedimentation can be common in the impounded sections of dammed rivers. Erosion of relict land surfaces that remained above the raised impounded water levels has been the dominant change in UMR impounded sections due to increased wind fetch leading to increased wave action. Even though upland sources of sediment from tributaries have decreased over the middle to late 20th century, increased annual precipitation, the interplay of increased variability in flood magnitudes from year to year, and more fall and winter flooding have likely changed erosion and sedimentation patterns in the UMR (Belby, et al., 2019). Paradoxically, monitoring and research indicates that the concentration of some water column constituents like total suspended solids and phosphorous has decreased during the 1991 to 2014 time period (Kreiling and Houser, 2016). In areas prone to increased sedimentation, bed elevations rise and thereby water depths are reduced at a given discharge, resulting in loss of fish habitat. Sediment deposition or erosion further influences water exchange rates between main channel and off-channel areas in the river by increasing resistance in connecting channels or enlarging existing connecting channels. Water depth and water exchange rates are the most prominent features describing habitat quality in the UMR (De Jager et al. 2018), and in some cases, the trajectory of planform change from heightened deposition promises to threaten deep backwater habitats particularly important for overwintering fish. Although information on the rate of vertical change in bed elevation is needed for a complete assessment of geomorphic change associated with the loss of deep backwater habitats, mapping planform changes over time (i.e., lateral changes between the land-water boundary) provide needed information on the location, potential cause, and progressive direction of deposition, especially in the mid sections between dams where deltaic processes are the most pronounced. Several types of planform changes have been observed and identified as concerns. For example, island loss in the large impounded areas of the upper part of the UMR was one of the concerns identified by river managers in the 1980s and 90s, and subsequently island construction became a common form of restoration implemented by the Upper Mississippi River Restoration (UMRR) Program (USACE 2012). Other subtler planform changes, such as channel bank erosion and delta formation in backwaters, are perceived to be important, but have largely gone unquantified. A systemwide reconnaissance of the UMR and IWW conducted in 1998 concluded that 14-percent of the river banks were eroding (Nakato and Anderson 1998). However, stabilization of existing river banks has never been widely pursued as a restoration measure, due to the high cost and uncertain benefits. Delta formation reduces the amount of backwater habitat; however, the deltas maintain and create a mix of riparian and aquatic habitats, and that is generally considered to be beneficial for wildlife and fish. If recent hydrologic trends of more frequent and longer duration flood events continue, a better understanding of planform changes can help in describing past changes, and then be used to forecast potential future trajectories of change. If UMR resource managers determine that past and forecasted conditions are undesirable, then UMRR projects could be identified and prioritized to address those concerns. Vegetative cover associations with landform changes have been used to detect and quantify planform changes in many rivers (Johnson 1985; Hiatt 2015; Volte et al. 2015). Freyer and Jefferson (2013) completed such a study in Pool 6 of the UMR using the landcover data from 12 dates over a 115-yr period, including the 1989, 2000, and 2010/2011 landcover/use (LCU) data from the UMRR Program. Planform change detected over the last 20 years represented by the UMRR Program data best reflect present-day geomorphic patterns, rates and processes. Changes occurring prior to dam construction and changes occurring soon after dam construction are likely not the same as those happening now, 50-70 years after dam construction and creation of the impoundments (McHenry et al., 1984; Bhowmik and Adams, 1986; WEST Consultants, 2000). The LCU data from each of the 1989, 2000, and 2010/2011 imagery was developed using similar methods and is available in a Geographical Information System (GIS) for the entire UMR and therefore provides the opportunity for a more comprehensive planform change analysis. This study used GIS overlays of LCU classes to map and quantify changes in planform features over two periods, looking specifically for depositional areas where terrestrial and wetland vegetation expanded at the expense of open water. The land expansion was grouped into four possible process-based types common in large floodplain rivers, some following that used by Lewin et al. (2017). The four types include: crevasse deltas emanating from a breach from a main channel through a natural levee or narrow floodplain into backwaters (crevasse deltas), tributary deltas expanding into backwaters (tributary deltas), deltaic bars at the upstream end of impoundments (impounded deltas), and linear-like bars extending from the downstream ends of narrow levees and remnant floodplains (bar-tail limbs). The methods deployed for change detection addressed possible errors from a variety of sources.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗
USGS2021

Evaluation of a “trace” plant density score in LTRM vegetation monitoring

The Long Term Resource Monitoring (LTRM) element of the Upper Mississippi River Restoration program employs a harvest method for sampling submersed aquatic vegetation (SAV) whereby a rake is dragged ~1.5 m over the substrate and plant materials are retrieved. “Plant density” (PD) scores indicate SAV abundance and are based on the amount of plant material collected on the teeth of the rake. Standard PD scores are ordered, whole numbers from 0 (no SAV on the rake) to 5 (80-100% of rake teeth full) and are assigned at each subsite for all species combined and for each individual species. In LTRM monitoring between 1998 and 2018, ~73% of non-zero, all-species-combined PD scores were 1s, and ~89% of individual SAV species were 1s. The preponderance of PD = 1 scores along with the wide range of fresh mass represented by PD = 1 (quantified in Drake and Lund 2020) limits inference about SAV abundance from LTRM monitoring data. Field personnel noted that small plant fragments comprised a substantial fraction of PD = 1 observations and proposed a modification of the existing LTRM methods where PD = 1 was subdivided to include “trace” scores to represent such small fragments. Trace was defined as PD = 0.08, indicating a maximum of 1 of 13 gaps in the sampling rake filled to the level of an original PD = 1. Amounts of plant material greater than PD = 0.08 and up to the original score of 1 were defined PD = +1. This study used field data collected in 2018 (scoring and fresh weights of scored plant materials) from 136 vegetated sites in Pools 4, 8 and 13 to evaluate the proposed subdivision and to examine among-pool differences in PD data. In the study data, 33% of all-species-combined observations and 69% of species (grouped by morphology) that would previously have received a score of 1 were classified as PD = 0.08. PD scores of 0.08, +1, and 2-3 represented statistically distinct amounts of fresh mass in rake samples. There were systematic differences in the mass of SAV reflected by PD score based on plant morphology and species composition. The mean fresh mass of plant materials assigned a given PD score varied among the three pools, suggesting bias attributable to personnel. To reduce this bias in future data collection efforts, the field crews incorporated a calibration of plant density scores in annual field training. The results presented here describe how including a trace PD score in LTRM data collection improves the description of SAV abundance and consequently estimates of biomass from those PD scores. LTRM vegetation crews have recorded trace scores in annual sampling since 2019 as extra information (i.e. which does not change the LTRM data stream as 0.08 and +1 scores can still be combined for PD=1). Trace data are not currently available to outside users through the LTRM data browser but are available from vegetation component personnel upon request.

Long Term Resource Monitoring Technical Report↗
USGS2010

Evaluation of light penetration on Navigation Pools 8 and 13 of the Upper Mississippi River

The availability of light can have a dramatic affect on macrophyte and phytoplankton abundance in virtually all aquatic ecosystems. The Long Term Resource Monitoring Program and other monitoring programs often measure factors that affect light extinction (nonvolatile suspended solids, volatile suspended solids, and chlorophyll) and correlates of light extinction (turbidity and Secchi depth), but rarely do they directly measure light extinction. Data on light extinction, Secchi depth, transparency tube, turbidity, total suspended solids, and volatile suspended solids were collected during summer 2003 on Pools 8 and 13 of the Upper Mississippi River. Regressions were developed to predict light extinction based upon Secchi depth, transparency tube, turbidity, and total suspended solids. Transparency tube, Secchi depth, and turbidity all showed strong relations with light extinction and can effectively predict light extinction. Total suspended solids did not show as strong a relation to light extinction. Volatile suspended solids had a greater affect on light extinction than nonvolatile suspended solids. The data were compared to recommended criteria established for light extinction, Secchi depth, total suspended solids, and turbidity by the Upper Mississippi River Conservation Committee to sustain submersed aquatic vegetation in the Upper Mississippi River. During the study period, the average condition in Pool 8 met or exceeded all of the criteria whereas the average condition in Pool 13 failed to meet any of the criteria. This report provides river managers with an effective tool to predict light extinction based upon readily available data.

Long Term Resource Monitoring Program Technical Re↗
USGS2010

Status and trends of selected resources in the Upper Mississippi River System

Like other large rivers, the Upper Mississippi River System (UMRS) serves a diversity of roles. The UMRS provides commercial and recreational fishing, floodplain agriculture, drinking water for many communities, an important bird migration pathway, a variety of recreational activities, and a navigation system that transports much of the country's agricultural exports. These multiple roles present significant management challenges. Regular assessment of the condition of the river is needed to improve management plans and evaluate their effectiveness. This report provides a summary of the recent status (mean and range of conditions) and trends (change in direction over time) for 24 indicators of the ecological condition of the Upper Mississippi and Illinois Rivers using data collected through the Long Term Resource Monitoring Program (LTRMP). The 24 indicators were grouped into seven categories: hydrology, sedimentation, water quality, land cover, aquatic vegetation, invertebrates, and fish. Most of the data used in the report were collected between about 1993 and 2004, although some older data were also used to compare to recent conditions.Historical observations and current LTRMP data clearly indicate that the UMRS has been changed by human activity in ways that have diminished the ecological health of the river. The data indicate that status and trends differ among regions, and we expect that regional responses to various ecological rehabilitation techniques will differ as well. The continuing role of the LTRMP will be to provide the data needed to assess changes in river conditions and to determine how those changes relate to management actions, natural variation, and the overall ecological integrity of the river system.

Long Term Resource Monitoring Program Technical Re↗
USGS2014

Spatially explicit habitat models for 28 fishes from the Upper Mississippi River System (AHAG 2.0)

Environmental management actions in the Upper Mississippi River System (UMRS) typically require pre-project assessments of predicted benefits under a range of project scenarios. The U.S. Army Corps of Engineers (USACE) now requires certified and peer-reviewed models to conduct these assessments. Previously, habitat benefits were estimated for fish communities in the UMRS using the Aquatic Habitat Appraisal Guide (AHAG v.1.0; AHAG from hereon). This spreadsheet-based model used a habitat suitability index (HSI) approach that drew heavily upon Habitat Evaluation Procedures (HEP; U.S. Fish and Wildlife Service, 1980) by the U.S. Fish and Wildlife Service (USFWS). The HSI approach requires developing species response curves for different environmental variables that seek to broadly represent habitat. The AHAG model uses species-specific response curves assembled from literature values, data from other ecosystems, or best professional judgment. A recent scientific review of the AHAG indicated that the model’s effectiveness is reduced by its dated approach to large river ecosystems, uncertainty regarding its data inputs and rationale for habitat-species response relationships, and lack of field validation (Abt Associates Inc., 2011). The reviewers made two major recommendations: (1) incorporate empirical data from the UMRS into defining the empirical response curves, and (2) conduct post-project biological evaluations to test pre-project benefits estimated by AHAG. Our objective was to address the first recommendation and generate updated response curves for AHAG using data from the Upper Mississippi River Restoration-Environmental Management Program (UMRR-EMP) Long Term Resource Monitoring Program (LTRMP) element. Fish community data have been collected by LTRMP (Gutreuter and others, 1995; Ratcliff and others, in press) for 20 years from 6 study reaches representing 1,930 kilometers of river and >140 species of fish. We modeled a subset of these data (28 different species; occurrences at sampling sites as observed in day electrofishing samples) using multiple logistic regression with presence/absence responses. Each species’ probability of occurrence, at each sample site, was modeled as a function of 17 environmental variables observed at each sample site by LTRMP standardized protocols. The modeling methods used (1) a forward-selection process to identify the most important predictors and their relative contributions to predictions; (2) partial methods on the predictor set to control variance inflation; and (3) diagnostics for LTRMP design elements that may influence model fits. Models were fit for 28 species, representing 3 habitat guilds (Lentic, Lotic, and Generalist). We intended to develop “systemic models” using data from all six LTRMP study reaches simultaneously; however, this proved impossible. Thus, we “regionalized” the models, creating two models for each species: “Upper Reach” models, using data from Pools 4, 8, and 13; and “Lower Reach” models, using data from Pool 26, the Open River Reach of the Mississippi River, and the La Grange reach of the Illinois River. A total of 56 models were attempted. For any given site-scale prediction, each model used data from the three LTRMP study reaches comprising the regional model to make predictions. For example, a site-scale prediction in Pool 8 was made using data from Pools 4, 8, and 13. This is the fundamental nature and trade-off of regionalizing these models for broad management application. Model fits were deemed “certifiably good” using the Hosmer and Lemeshow Goodness-of-Fit statistic (Hosmer and Lemeshow, 2000). This test post-partitions model predictions into 10 groups and conducts inferential tests on correspondences between observed and expected probability of occurrence across all partitions, under Chi-square distributional assumptions. This permits an inferential test of how well the models fit and a tool for reporting when they did not (and perhaps why). Our goal was to develop regionalized models, and to assess and describe circumstances when a good fit was not possible. Seven fish species composed the Lentic guild. Good fits were achieved for six Upper Reach models. In the Lower Reach, no model produced good fits for the Lentic guild. This was due to (1) lentic species being much less prominent in the Lower Reach study areas, and (2) those that do express greater prominence principally do so only in the La Grange reach of the Illinois River. Thus, developing Lower Reach models for Lentic species will require parsing La Grange from the other two Lower Reach study areas and fitting separate models. We did not do that as part of this study, but it could be done at a later time. Nine species comprised the Lotic guild. Good fits were achieved for seven Upper Reach models and six Lower Reach models. Four species had good fits for both regions (flathead catfish, blue sucker, sauger, and shorthead redhorse). Three species showed zoogeographic zonation, with a good model fit in one of the regions, but not in the region in which they were absent or rarely occurred (blue catfish, rock bass, and skipjack herring). Twelve species comprised the Generalist guild. Good fits were achieved for five Upper Reach models and eight Lower Reach models. Six species had good fits for both regions (brook silverside, emerald shiner, freshwater drum, logperch, longnose gar, and white bass). Two species showed zoogeographic zonation, with a good model fit in one of the regions, but not in the region in which they were absent or rarely occurred (red shiner and blackstripe topminnow). Poorly fit models were almost always due to the diagnostic variable “field station,” a surrogate for river mile. In these circumstances, the residuals for “field station” were non-randomly distributed and often strongly ordered. This indicates either fitting “pool scale” models for these species and regions, or explicitly model covariances between “field station” and the other predictors within the existing modeling framework. Further efforts on these models should seek to resolve these issues using one of these two approaches. In total, nine species, representing two of the three guilds (Lotic and Generalist), produced well-fit models for both regions. These nine species should comprise the basis for AHAG 2.0. Additional work, likely requiring downscaling of the regional models to pool-scale models, will be needed to incorporate additional species. Alternately, a regionalized AHAG could be comprised of those species, per region, that achieved well-fit models. The number of species and the composition of the regional species pools will differ among regions as a consequence. Each of these alternatives has both pros and cons, and managers are encouraged to consider them fully before further advancing this approach to modeling multi-species habitat suitability.

Upper Mississippi River System↗
USGS2014

Relationship of weed shiner and young-of-year bluegill and largemouth bass abundance to submersed aquatic vegetation in Navigation Pools 4, 8, and 13 of the Upper Mississippi River, 1998-2012

Aquatic vegetation provides food resources and shelter for many species of fish. This study found a significant relationship between increases in submersed aquatic vegetation (SAV) in four study reaches of the Upper Mississippi River (UMR) and increases in catch-per-unit-effort (CPUE) of weed shiners ( Notropis texanus ) and age-0 bluegills ( Lepomis macrochirus ) and largemouth bass ( Micropterus salmoides ) when all of the study reaches were treated collectively using Long Term Resource Monitoring Program (LTRMP) vegetation and fish data for 1998–2012. The selected fishes were more abundant in study reaches with higher SAV frequencies (Pool 8 and Lower Pool 4) and less abundant in reaches with lower SAV frequencies (Pool 13 and Upper Pool 4). When each study reach was examined independently, the relationship between SAV frequency and CPUE of the three species was not significant in most cases, the primary exception being weed shiners in Lower Pool 4. Results of this study indicate that the prevalence of SAV does affect relative abundance of these vegetation-associated fish species. However, the poor annual relationship between SAV frequency and age-0 relative abundance in individual study reaches indicates that several other factors also govern age-0 abundance. The data indicate that there may be a SAV frequency threshold in backwaters above which there is not a strong relationship with abundance of these fish species. This is indicated by the high annual CPUE variability of the three selected fishes in backwaters of Pool 8 and Lower Pool 4 when SAV exceeded certain frequencies.

Upper Mississippi River↗
USGS2004

A suspended sediment budget for Pool 13 and La Grange Pool of the upper Mississippi River system

The suspended sediment budget for Pool 13 of the Mississippi River and La Grange Pool of the Illinois River was examined over a 3-yr period (October 1995 through September 1997). Pool 13 output was between 3.07 and 3.64 million t (metric tons) of suspended sediment annually during the study period. Loads to Pool 13 were dominated by those delivered by the Mississippi River (76%, 74%, and 66% in the 1995, 1996, and 1997 water years, respectively). Pool 13 exhibited sediment export (output greater than input) in 1995, a balance in 1996, and marked sediment trapping (output less than input) in 1997. Within the three study years, Pool 13 received its highest water and sediment loads during spring (March through May) and this period was marked by sediment export. Suspended sediment loads were trapped during the remainder of the year. La Grange Pool output was between 3.71 and 5.04 million t of suspended sediment annually during the 1995-97 water years. The Illinois River accounted for less than 50% of the suspended sediment load to the pool (19%, 25%, and 45% in the 1995, 1996, and 1997 water years, respectively. La Grange Pool exhibited considerable sediment trapping in 1995 whereas the 1996 and 1997 water years were much closer to a balance wherein output was within 5% of input. Generally, La Grange Pool received its largest water and sediment loads during the late spring—early summer period (April through June), but in 1997 the late winter loads predominated. In all years, La Grange Pool trapped the sediments during these high discharge, high loading periods and exported suspended sediments for the remainder of the year. The distinct differences in the manner in which these pools process suspended sediment loads may be related to the considerable differences between the morphometry of these pools.

Illinois, Iowa↗
USGS1999

Pool 13 drawdown: Predicting success rates and affected areas

The likelihood of 1- or 2-foot drawdowns, and the area affected by such alternative drawdowns, was estimated for Pool 13 on the Upper Mississippi River. Minimum water surface (elevation) requirements were compared to computed water surface profiles to determine a critical low flow that would allow a navigation channel 400 feet wide and 10.5 feet deep. An upper limit on flow was established based on the flow at which open river conditions would exist for a given drawdown. The range in flows that would allow for a drawdown was used to estimate success rates using historical daily discharge data. Success rates were determined for a variety of drawdown durations between two time periods. May 1—August 15 and June 15—August 15. The greatest effect of the drawdown would he near Lock and Dam 13. Higher discharges, as well as distance from the dam. lessen the drawdown amount. Areas that would he affected by these two drawdown scenarios were predicted by overlaying maps of water surfaces with depths using a geographic information system. Although the drawdown effects on most physical and biotic components of Pool 13 arc unknown, some general drawdown effects likely to occur because of the changes in water surface elevation are presented.

Illinois, Iowa↗
USGS2022

Contaminants of emerging concern in the Great Lakes: Science to inform management practices for protecting the health and integrity of wildlife populations from adverse effects: GLRI action plan I, focus area 1, goal 5

Executive Summary: Under Action Plan I (2010-2014) of the Great Lakes Restoration Initiative (GLRI), Federal and Academic partners began an investigation of the presence and distribution of contaminants of emerging concern (CECs) in the Great Lakes and potential impacts on fish and wildlife. The term CECs is applied to a broad range of chemicals that are currently in use but for which we currently lack good understanding of whether fish, wildlife, or humans are being exposed and/or whether negative health or environmental effects are expected if exposure occurs. Pharmaceuticals, personal care products, flame retardants, many current use pesticides, and poly- and perfluorinated chemicals are some well-known groups of CECs, but there is no definitive or comprehensive list that can be used to support the management of CECs to reduce impacts on the Great Lakes ecosystem. Four overarching goals were identified for this collaborative investigation: 1. Evaluate the sources, occurrence, and distribution of CECs across the Great Lakes Basin. 2. Examine associations between the distribution of CECs and land-use patterns. 3. Review both scientific literature and field-generated data to determine the potential for CECs to cause adverse effects on Great Lakes fish and wildlife populations. 4. Develop efficient strategies to survey and/or monitor for threats that CECs may pose in order to take effective management actions before those threats evolve into large scale impacts on Great Lakes ecosystems or the services they provide. Achievement of these goals ensures progress towards Focus Area 1: Toxic Substances and Areas of Concern from GLRI Action Plan I, Goal 5: “ The health and integrity of wildlife populations and habitat are protected from adverse chemical and biological effects associated with the presence of toxic substances in the Great Lakes Basin ”. This large-scale research effort was comprised of individual and collaborative projects from multiple federal agencies and academic institutions, involving over 85 investigators, and overseen by the U.S. Environmental Protection Agency (EPA) Region 5, Great Lakes National Program Office. Partners include the United States Geological Survey, the National Oceanic and Atmospheric Administration, U.S. Fish and Wildlife Service, Saint Cloud State University, the U.S. EPA Office of Research and Development, and the U.S. Army Corps of Engineers. Key findings: 1. Contaminants of emerging concern were found throughout the monitored Great Lakes tributaries, but types and concentrations vary in association with regional land use. CECs were detected in nearly all samples collected. The type and concentration of the specific contaminants detected varied considerably among field sites and in association with land use type, such as urban, agricultural, wetland, 2 or forest. Contaminants were detected in the water column, sediment, and tissues of all species surveyed in the current work (mussels, aquatic insects, fish, and insect-eating birds). 2. There were over 20 contaminants for which CEC concentrations approached or exceeded those reported to cause toxicity in laboratory experiments. This was based on detection in water, sediments and or biota at one or more field sites. These contaminants represent compounds that warrant further investigation and monitoring with respect to potential impacts in certain areas of the Great Lakes basin. Based on the present investigation, compounds of greatest concern include: polycyclic aromatic hydrocarbons, associated with oil-based products and combustion of organic matter; atrazine, an herbicide; dichlorvos, an insecticide; and ibuprofen and venlafaxine, both pharmaceuticals. 3. Results suggest that mixtures of CECs presently found in most Great Lakes tributary locations surveyed may elicit subtle biological effects, but likely are not, alone, causing obvious detriment to current communities of fish and wildlife. CECs detected in the Great Lakes were associated with subtle biological effects like changes in gene expression, altered circulating glucose, etc. in both wild-caught and laboratory-reared organisms. These effects were generally not indicative of reproductive failure or mortality. However, the effects may have more serious implications when combined with other sources of stress like habitat degradation, changing climate conditions, and competition with invasive species. Due to limited historical data, it is unknown whether severe CEC-related impacts have already affected aquatic communities in waterbodies that have received long-term inputs of these contaminants. Likewise, under Action Plan I, biological effects were not necessarily evaluated at the sites where CEC concentrations exceeding laboratory toxicity thresholds were detected. As a result, strategic, ongoing surveillance and monitoring of CECs is warranted. This collaborative investigation resulted in new tools, approaches, and data that can be used to inform and support the management of CECs to reduce their impacts on Great Lakes natural resources. The following products of this research effort are available through https://communities.geoplatform.gov/glri/ or by contacting the investigators (see technical chapters found in Appendices A-F): 1. Database of CEC occurrence and concentrations in US tributary streams. The database includes CEC detections in water, sediment, and fish and wildlife tissues, and represents the most comprehensive survey of CECs in the Great Lakes Region. 2. Synopses of results and key findings. Integrated summaries of results, conclusions, and management implications of the CEC research are available through reports, topical fact sheets, and presentations. 3. Technical publications: This collaborative research effort has resulted in over 50 peer-reviewed publications, agency reports, and data releases that can be of use to resource managers, the scientific community, and members of the public. 4. Innovative tools. Innovative monitoring devices, sampling equipment, conceptual frameworks, and software applications were developed over the course of this 3 research. These tools are transferable to stakeholders via internet accessibility or via specifications, instructions, and demonstration detailed in technical publications. Hypotheses to guide CECs research under Action Plan II. Findings from 2010-2014 were used to guide further research in 2015-2018 for basin-wide surveillance of CECs and for sites warranting further study of potential biological impacts of CECs. Additional surveillance included both evaluation of additional classes of contaminants and expanded lists for chemical classes shown to be of greatest concern. Mixtures of some of the most frequently detected contaminants were also tested in laboratory studies to understand whether long term exposures to multiple contaminants may result in effects not evident from uncontrolled, short-term field experiments.

Great Lakes↗
USGS1996

Summary of hydrogeologic controls on ground-water flow at the Nevada Test Site, Nye County, Nevada

The underground testing of nuclear devices has generated substantial volumes of radioactive and other chemical contaminants below ground at the Nevada Test Site (NTS). Many of the more radioactive contaminants are highly toxic and are known to persist in the environment for thousands of years. In response to concerns about potential health hazards, the U.S. Department of Energy, under its Environmental Restoration Program, has made NTS the subject of a long-term investigation. Efforts supported through the U.S. Department of Energy program will assess whether byproducts of underground testing pose a potential hazard to the health and safety of the public and, if necessary, will evaluate and implement steps to remediate any of the identified dangers. Test-generated contaminants have been introduced over large areas and at variable depths above and below the water table throughout NTS. Evaluating the risks associated with these byproducts of underground testing presupposes a knowledge of the source, transport, and potential receptors of these contaminants. Ground-water flow is the primary mechanism by which contaminants can be transported significant distances away from the initial point of injection. Flow paths between contaminant sources and potential receptors are separated by remote areas that span tens of miles. The diversity and structural complexity of the rocks along these flow paths complicates the hydrology of the region. Although the hydrology has been studied in some detail, much still remains uncertain about flow rates and directions through the fractured-rock aquifers that transmit water great distances across this arid region. Unique to the hydrology of NTS are the effects of underground testing, which severely alter local rock characteristics and affect hydrologic conditions throughout the region. Any assessment of the risk must rely in part on the current understanding of ground-water flow, and the assessment will be only as good as the understanding itself. This report summarizes what is known and inferred about ground-water flow throughout the NTS region. The report identifies and updates what is known about some of the major controls on ground-water flow, highlights some of the uncertainties in the current understanding, and prioritizes some of the technical needs as related to the Environmental Restoration Program. An apparent deficiency in the current understanding is a lack of knowledge about flow directions and rates away from major areas of testing. Efforts are necessary to delineate areas of downgradient flow and to identify factors that constrain and control flow within these areas. These efforts also should identify the areas most critical to gaining detailed understanding and to establishing long-term monitoring sites necessary for effective remediation.

Nevada↗
USGS1989

U.S. Geological Survey second national symposium on Water quality; abstracts of the technical sessions, Orlando, Florida, November 12-17, 1989

The U.S Geological Survey (USGS) compiled and analyzed existing hydrologic and water-quality data from over 200 stream and estuary stations of the Abemarle-Pamlico estuarine system (A/P) to identify long-term temporal and spatial trends. The dataset included seven stations of the USGS National Stream Quality Accounting Network, two stations of the National Atmospheric Precipitation Deposition monitoring network, stations of the N.C. Department of Natural Resources and Community Development, and stations from 25 reports by individual investigators. Regression-residuals analysis, the seasonal Kendall's Tau test for trends, and graphical analysis using annual box plots were employed to determine trends. Profound change has occurred in the water quality of the A/P area over the last 30 years. Analysis of water-quality data upstream from the estuaries indicates increases of discharge-adjusted values of specific conductance, alkalinity, phosphorous, hardness, chloride, and dissolved solids. In the estuaries, pH is increasing except in the Pamlico River, where it is decreasing. There is a generalized decrease in suspended inorganic material in the system. Salinities are decreasing for sections of the Pamlico River, and increasing for parts of Albemarle Sound. Nitrogen concentrations are decreasing except in the Pamlico River, where they are increasing. Phosphorus concentrations are increasing in the Pamlico River and decreasing elsewhere. Annual average data show that nitrogen is the limiting nutrient in the Neuse and Pamlico Rivers. Phosphorus is limiting in the rest of the area. Chlorophyll-a levels are increasing in parts of the Neuse and Pamlico Rivers and decreasing in parts of the Chowan River. To evaluate the effect of basin characteristics on water quality, linear correlation was used. Agricultural crop variables produced the most correlations with water-quality data. Fertilizer usage had little detectable relation to water quality in the study area. In the section of the Pamlico River near Aurora, relations between employment, road mileages, and water quality indicated effects of development in the area.

Open-File Report↗
USGS2004

Designing monitoring programs in an adaptive management context for regional multiple species conservation plans

Increasing numbers of regional, multiple species conservation plans have been developed in California since the early 1990s. However, building effective monitoring and adaptive management programs to support these plans has remained a challenge. In addition to collecting data on the status of resources and the results of management actions, monitoring programs for these plans need to resolve critical uncertainties and channel information into effective decisionmaking. Because of the broad goals of many regional conservation plans, monitoring programs need to address ecosystem integrity and biodiversity while also tracking species ?covered? by plan permits. In this document we provide a step-by-step procedure for developing effective monitoring programs in an adaptive management context. The guidance provided here has been gleaned from experience with large multiple species plans in southern California. The process begins with clearly defining program objectives, partitioning the program into manageable but meaningful pieces, and developing management-oriented conceptual models of system function. Then, based on the objectives and conceptual models, monitoring recommendations and critical uncertainties can be identified and a coordinated program designed. We include practical examples and insights from programs in southern California and discuss the evolution of monitoring and adaptive management programs through three successive stages: 1) inventorying resources and identifying relationships; 2) pilot testing of long-term monitoring and resolving critical management uncertainties; and 3) implementing long-term monitoring and adaptive management. Ultimately, the success of regional conservation planning depends on the ability of monitoring programs to confront the challenges of adaptively managing and monitoring complex ecosystems and diverse arrays of sensitive species.

Technical Report↗
USGS2011

U.S. Geological Survey Science for the Wyoming Landscape Conservation Initiative-2010 Annual Report

This is the third report produced by the U.S. Geological Survey (USGS) for the Wyoming Landscape Conservation Initiative (WLCI) to detail annual work activities. The first report described activities for 2007 and 2008, and the second report covered work activities for FY09. This third report covers work activities conducted in FY2010, and it continues the 2009 approach of reporting on all the individual activities to help give WLCI partners and other readers the full scope of what has been accomplished. New in this year's report is an additional section for each work activity that outlines the work planned for the following fiscal year. In FY2010, there were 35 ongoing/expanded, completed, or new projects conducted under the five major multi-disciplinary science and technical-assistance activities: (1) Baseline Synthesis; (2) Targeted Monitoring and Research; (3) Data and Information Management; (4) Integration and Coordination; and (5) Decisionmaking and Evaluation. The three new work activities were to (1) compile existing water data for the entire WLCI region and (2) develop regional curves (statistical models) for relating bankfull-channel geometry and discharge to drainages in the WLCI region, both of which will help guide long-term monitoring of water resources; and (3) initiate a groundwater-monitoring network to evaluate potential effects of energy-development activities on groundwater quality where groundwater is an important source of public/private water supplies. Results of the FY2009 work to develop methods for assessing soil organic matter and mercury indicated that selenium and arsenic levels may be elevated in the Muddy Creek Basin; thus, the focus of that activity was shifted in FY2010 to evaluate biogeochemical cycling of elements in the basin. In FY2010, two ongoing activities were expanded with the addition of more sampling plots: (a) the study of how greater sage-grouse (Centrocercus urophasianus) use vegetation-treatment areas (sites added to the Moxa Arch Natural Gas Development area) and (2) the study of cheatgrass (Bromus tectorum) occurrence in burn treatments of the Little Mountain Ecosystem. The activity that entails evaluating relationships between ungulate herbivory and fire on aspen (Populus tremuloides) recruitment also was expanded to include relationships between stand characteristics of and herbivory on aspen in various ecohydrological settings. The USGS continued compiling data and developing geospatial products from all of its WLCI activities to support (1) ranking and prioritizing of proposed conservation projects, (2) developing the WLCI Integrated Assessment, and (3) developing the WLCI 5-year Conservation Action Plan. Two activities were completed in FY2010: (1) the conceptual modeling and indicator selection for monitoring resource conditions across the WLCI region, and (2) the literature review on effects of oil and gas development in western regions of the United States, both of which are in the last stages of publication.

Open-File Report↗