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USGS2015

Validation of a spatial model used to locate fish spawning reef construction sites in the St. Clair–Detroit River system

Lake sturgeon ( Acipenser fulvescens ) populations have suffered precipitous declines in the St. Clair–Detroit River system, following the removal of gravel spawning substrates and overfishing in the late 1800s to mid-1900s. To assist the remediation of lake sturgeon spawning habitat, three hydrodynamic models were integrated into a spatial model to identify areas in two large rivers, where water velocities were appropriate for the restoration of lake sturgeon spawning habitat. Here we use water velocity data collected with an acoustic Doppler current profiler (ADCP) to assess the ability of the spatial model and its sub-models to correctly identify areas where water velocities were deemed suitable for restoration of fish spawning habitat. ArcMap 10.1 was used to create raster grids of water velocity data from model estimates and ADCP measurements which were compared to determine the percentage of cells similarly classified as unsuitable, suitable, or ideal for fish spawning habitat remediation. The spatial model categorized 65% of the raster cells the same as depth-averaged water velocity measurements from the ADCP and 72% of the raster cells the same as surface water velocity measurements from the ADCP. Sub-models focused on depth-averaged velocities categorized the greatest percentage of cells similar to ADCP measurements where 74% and 76% of cells were the same as depth-averaged water velocity measurements. Our results indicate that integrating depth-averaged and surface water velocity hydrodynamic models may have biased the spatial model and overestimated suitable spawning habitat. A model solely integrating depth-averaged velocity models could improve identification of areas suitable for restoration of fish spawning habitat.

Michigan↗

USGS2020

Review of trap-and-haul for managing Pacific salmonids (Oncorhynchus spp.) in impounded river systems

High-head dams are migration barriers for Pacific salmon Oncorhynchus spp. in many river systems and recovery measures for impacted stocks are limited. Trap-and-haul has been widely used in attempts to facilitate recovery but information from existing programs has not been synthesized to inform improvements to aid recovery of salmonids in systems with high-head dams. We reviewed 17 trap-and-haul programs regarding Pacific salmon to: (1) summarize information about facility design, operation and biological effects; (2) identify critical knowledge gaps; and (3) evaluate trap-and-haul as a current and future management tool. Existing programs are operated to address a range of management goals including restoring access to historical habitats, temporarily reducing exposure to dangerous in-river conditions, and reintroducing ecological processes upstream from dams. Information gathered from decades of operation on facility design criteria and fish handling protocols, and robust literature on fish collection and passage are available. While many aspects of trap-and-haul have been evaluated, effects on population productivity and sustainability remain poorly understood. Long-term and systematic studies of trap-and-haul outcomes are rare, and assessments can be confounded by concurrent management actions and broad ecological and climatic effects. Existing data suggest that performance and effectiveness vary among programs and over various time scales within programs. Although critical information gaps exist, trap-and-haul is an important management and conservation tool for providing Pacific salmonids access to historical habitats. Successful application of trap-and-haul programs requires long-term commitment and an adaptive management approach by dam owners and stakeholders, and careful planning of new programs.

California, Idaho, Oregon, Washington↗

USGS2014

A model to locate potential areas for lake sturgeon spawning habitat construction in the St. Clair–Detroit River System

In response to a need for objective scientific information that could be used to help remediate loss of fish spawning habitat in the St. Clair River and Detroit River International Areas of Concern, this paper summarizes a large-scale geographic mapping investigation. Our study integrates data on two variables that many riverine fishes respond to in selecting where to spawn in these waters (water flow velocity and water depth) with available maps of the St. Clair–Detroit River System (SC–DRS). Our objectives were to locate and map these two physical components of fish habitat in the St. Clair and Detroit rivers and Lake St. Clair using a geographic information system (GIS) and to identify where, theoretically, fish spawning habitat could be remediated in these rivers. The target fish species to which this model applies is lake sturgeon (Acipenser fulvescens), but spawning reefs constructed for lake sturgeon in this system have been used for spawning by 17 species of fish. Our analysis revealed areas in each river that possessed suitable water velocity and depth for fish spawning and therefore could theoretically be remediated by the addition of rock-rubble substrate like that used at two previously remediated sites in the Detroit River at Belle Isle and Fighting Island. Results of our analysis revealed that only 3% of the total area of the SC–DRS possesses the necessary combination of water depth and high flow velocity to be indicated by the model as potential spawning habitat for lake sturgeon.

Michigan, Ontario↗

USGS2022

Identifying and characterizing juvenile lake sturgeon (Acipenser fulvescens, Rafinesque, 1817) occupancy hot spots within the St. Clair-Detroit River System

Over the past two decades, extensive monitoring has been conducted in the St. Clair – Detroit River System to describe spatial and temporal patterns of lake sturgeon ( Acipenser fulvescens ). To characterize spatial patterns in juvenile lake sturgeon (<1000 mm TL) based on survey collections, ‘hot spots’ were identified through optimized hot spot analysis (HSA). This HSA was then interpolated by inverse distance weighted analysis to determine extent of identified ‘hot spots’ and ‘cold spots’. Additionally, habitat variables (i.e., water depth, water velocity, and dominant substrate type) were investigated using a single season occupancy model to determine their influence on juvenile lake sturgeon occupancy probability. In total, 1203 juvenile lake sturgeon were captured across 4197 surveys. Three unique ‘hot spots’ were identified; western Lake Erie, Fighting Island in the Detroit River, and the North Channel in the St. Clair River. Interpolated ‘hot spots’ encompassed 73.1 km² in western Lake Erie, 4.7 km² near Fighting Island, and 6.6 km² in the North Channel. Detection probabilities within ‘hot spots’ ranged from 8.8%–43.4%. No habitat variables significantly predicted juvenile lake sturgeon occupancy. Juvenile lake sturgeon were captured in western Lake Erie where the water depth was >5.1 m and odds of occupancy increased with increased water velocity. Juvenile lake sturgeon in the Detroit and St. Clair River ‘hot spots’ were captured at sites with mean benthic water velocities ranging from 0.20–0.60 m/s and where water depth was >7.3 m. Irrespective of waterbody, 69% of all juveniles were detected over dominant sand and gravel substrates. These results provide valuable insight about juvenile habitat use that can help managers formulate effective conservation and restoration strategies supporting the continued recovery of Great Lakes lake sturgeon.

Michigan↗

USGS2024

A video monitoring and computational system for estimating migratory juvenile fish abundance in river systems

Diadromous fishes migrate between marine and fresh waters for reproduction. For anadromous species, which spawn in freshwater, improved access to freshwater spawning and nursery habitats and ability of juveniles to emigrate to the ocean may support population recovery. Despite the potentially enormous influence of early life stage survival on adult population size, managers and scientists have limited capacity to assess numbers of juvenile anadromous fishes leaving freshwater ecosystems. Such data are critical for evaluating reproductive success and habitat suitability and have been identified as a top priority in anadromous fish research and management. We developed a state-of-the-art underwater video and computational system to collect videos to estimate abundances and migration timing for juvenile river herring ( Alosa pseudoharengus ; Alosa aestivalis ). We collected continuous video in the Monument River (Bourne, Massachusetts, USA) from June to November 2017. We trained three types of neural network models to detect and count fish in video frames and evaluated model performance by comparing human counts to model outputs. Our top model assessed presence and absence ( F 1 = 87%) and counted fish (counting error 9.4%) with an accuracy comparable to human counters ( F 1 = 88%). Our system's capability to collect accurate counts of emigrating juveniles will provide critical information that could be related to the numbers of spawning adults, system-specific productivity, and spawning and nursery habitat suitability. Both the video collection system and computational model may be transferrable to other sites and for other species where tracking juvenile emigration may inform management efforts.

Massachusetts↗

USGS2011

Spatial variation in fish species richness of the upper Mississippi River system

Important natural environmental gradients, including the connectivity of off-channel aquatic habitats to the main-stem river, have been lost in many reaches of the upper Mississippi River system, and an understanding of the consequences of this isolation is lacking in regard to native fish communities. The objectives of this study were to describe patterns of fish species richness, evenness, and diversity among representative habitats and river reaches and to examine the relationship between fish species richness and habitat diversity. Each year (1994-1999) fish communities of main-channel borders (MCB), side channel borders (SCB), and contiguous backwater shorelines (BWS) were sampled using boat-mounted electrofishing, mini-fyke-nets, tyke nets, hoop nets, and seines at a standardized number of sites. A total of 0.65 million fish were collected, representing 106 species from upper Mississippi River Pools 4, 8, 13, and 26; the open (unimpounded) river reach; and the La Grange Reach of the Illinois River. Within pools, species richness based on rarefaction differed significantly among habitats and was highest in BWS and lowest in MCB (P < 0.0001). At the reach scale, Pools 4, 8, and 13 consistently had the highest species richness and Pool 26, the open-river reach, and the La Grange Reach were significantly lower (P < 0.0001). Species evenness and diversity indices showed similar trends. The relationship between native fish species richness and habitat diversity was highly significant (r(2) = 0.85; P = 0.0091). These results support efforts aimed at the conservation and enhancement of connected side channels and backwaters. Although constrained by dams, pools with high native species richness could serve as a relative reference. The remnants of natural riverine dynamics that remain in these reaches should be preserved and enhanced; conditions could be used to guide restoration activities in more degraded reaches.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

USGS2025

Angler dynamics in the St. Clair-Detroit River System after decades of change

Habitat and water quality were historically degraded within the St. Clair-Detroit River System (SCDRS). Beginning in 2004, extensive habitat restoration projects were implemented remediating losses of fish spawning beds and shoreline areas. Monitoring of post-restoration activities documented recovering fish populations; however, angler response remains unknown. Extensive creel surveys were conducted pre-restoration (2002–2004), but post-restoration (2012 and later) surveys were intermittent. The goal of this project was to examine both to create a comprehensive picture of the effects of restoration on angling. We calculated catch and harvest rates and inspected answers to supplemental questions collected by state and provincial agencies. We estimated economic impact of angling with a combination of lodging and gas expenses. Post-restoration, catch rates were higher, but harvest rates were variable for Lake St. Clair and the Detroit River. The 2017 open water boat fishery on Lake St. Clair was worth ∼$26 million. Increased fishing opportunities resulting from continued habitat and population recovery are leading to increased catch rates and likely attracting anglers to the area.

Michigan, Ontario↗

USGS2025

Effects of nest exclosure on nest and adult survival of piping plover (Charadrius melodus) in the lower Platte River System, Nebraska

Conservation of imperiled species often includes management strategies intended to improve specific vital rates. However, some management practices can have unforeseen consequences that negate the intended benefit. For example, nest exclosures are often used for ground-nesting avian species to reduce nest predation but may increase depredation of adults. Tradeoffs between nest survival and adult mortality of nest exclosures likely depend on local predator community dynamics. Therefore, investigations are most informative when assessed in specific settings. Piping Plovers ( Charadrius melodus , hereafter plovers) in the lower Platte River system, Nebraska, nest at off-river sandpit sites, which provide an additional study system and habitat to assess the context-dependent effects of nest exclosures. The Tern and Plover Conservation Partnership monitors plovers at off-river sites by monitoring nests, installing nest exclosures, and banding and resighting. Effects of nest exclosures were tested on both nest survival, from 340 plover nests from 2008–2024, and weekly within-season apparent survival, from 71 breeding adults from 2011–2024. There was weak evidence that nest exclosures marginally improved nest survival but no evidence of an effect for within-season survival of breeding adults. Daily nest survival was slightly higher for exclosed nests (0.99, [85% CI = 0.98–0.99]) than unexclosed nests (0.98, [0.98–0.99]). Within-season apparent weekly survival for breeding plovers was 0.90 (95% CI = 0.83–0.93); cumulative survival over the breeding period was 0.51 (0.33–0.69). Nest exclosures may be used to increase nest survival at off-river sites with minimal threat to adult survival unless considerable concerns arise.

Nebraska↗

USGS2014

Verifying success of artificial spawning reefs in the St. Clair-Detroit River System for lake sturgeon ( Acipenser fulvescens Rafinesque, 1817)

Lake sturgeon ( Acipenser fulvescens ) were historically abundant in the St. Clair – Detroit River System (SCDRS), a 160 km river/channel network. In the SCDRS, lake sturgeon populations have been negatively affected by the loss/degradation of natural spawning habitat. To address habitat loss for lake sturgeon and other species, efforts are underway to restore spawning substrate by constructing artificial reefs. The main objective of this study was to conduct post-construction monitoring of lake sturgeon egg deposition and larval emergence near two of these artificial reefs: Fighting Island Reef (FIR) in the Detroit River, and Middle Channel Reef in the St. Clair River. An additional site in the St. Clair River where lake sturgeon spawn on a coal clinker bed was also investigated. From 2010 to 2012, viable eggs and larvae were collected from all of these reefs, indicating that conditions are suitable for egg deposition, incubation, and larval emergence. In the St. Clair River, the results indicate the likelihood of other spawning sites upstream of these artificial reef sites.

Detroit River, St. Clair River↗

USGS2013

Size-dependent trophic patterns of pallid sturgeon and shovelnose sturgeon in a large river system

This study compared patterns of δ 15 N and δ 13 C enrichment of pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon S. platorynchus in the Missouri River, United States, to infer their trophic position in a large river system. We examined enrichment and energy flow for pallid sturgeon in three segments of the Missouri River (Montana/North Dakota, Nebraska/South Dakota, and Nebraska/Iowa) and made comparisons between species in the two downstream segments (Nebraska/South Dakota and Nebraska/Iowa). Patterns in isotopic composition for pallid sturgeon were consistent with gut content analyses indicating an ontogenetic diet shift from invertebrates to fish prey at sizes of >500-mm fork length (FL) in all three segments of the Missouri River. Isotopic patterns revealed shovelnose sturgeon did not experience an ontogenetic shift in diet and used similar prey resources as small (<500-mm FL) pallid sturgeon in the two downstream segments. We found stable isotope analysis to be an effective tool for evaluating the trophic position of sturgeons within a large river food web.

Missouri River↗

USGS2019

Zooplankton dynamics in a Great Lakes connecting channel: Exploring the seasonal composition within the St. Clair-Detroit River System

The connecting channels linking the Laurentian Great Lakes provide important migration routes, spawning grounds, and nursery habitat for fish, but their role as conduits between lakes for zooplankton is less understood. To address this knowledge gap in the St. Clair–Detroit River System (SCDRS), a comprehensive survey of crustacean zooplankton was performed in both riverine and lacustrine habitats from spring to fall 2014, providing the first system-wide assessment of zooplankton in the SCDRS. Zooplankton density and biomass were greatest in northern reaches of the system (southern Lake Huron and the St. Clair River) and decreased downstream towards Lake Erie. The composition of zooplankton also changed moving downstream, transitioning from a community dominated by calanoid copepods, to more cyclopoids and cladocerans in the Detroit River, and to cladocerans dominant in western Lake Erie. Coincidentally, species richness increased as sampling progressed downstream, and we estimated that our single-year sampling regime identified ~88% of potential taxa. Other species assemblages have responded positively to recent water quality and habitat restoration efforts in the SCDRS, and this survey of the zooplankton community provides benchmark information necessary to assess its response to continued recovery. In addition, information regarding the lower trophic levels of the system is integral to understanding recruitment of ecologically and economically valuable fish species targeted for recovery in the SCDRS.

St. Clair-Detroit River System↗

USGS1986

Distribution of submersed macrophytes in the St. Clair-Detroit River System, 1978

An extensive survey was conducted in fall 1978 to determine the distribution and abundance of submersed macrophytes through the St. Clair-Detroit River system from Lake Huron to Lake Erie. Submersed macrophytes, representing 19 taxa, were widely distributed in the system, being found on 358 km 2 (30%) of the total 1185 km 2 of substrate surveyed. Of the 19 taxa identified, 8 common taxa were found on 20 to 121 km 2 of substrate. These commonly found taxa, in decreasing order of substrate coverage were Characeae, Vallisneria americana , Najas flexilis , Myriophyllum spicatum , Elodea canadensis , Potamogeton richardsonii , Potamogeton spp. (narrow-leaf forms), and Heteranthera dubia . In general, macrophyte beds of low, medium, and high biomass covered much less area but a higher proportion of the available substrate in the St. Clair and Detroit rivers than in Lake St. Clair.

Journal of Freshwater Ecology↗

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↗

USGS2014

Confocal microscopy as a useful approach to describe gill rakers of Asian species of carp and native filter-feeding fishes of the upper Mississippi River system

To better understand potential diet overlap among exotic Asian species of carp and native species of filter-feeding fishes of the upper Mississippi River system, microscopy was used to document morphological differences in the gill rakers. Analysing samples first with light microscopy and subsequently with confocal microscopy, the three-dimensional structure of gill rakers in Hypophthalmichthys molitrix , Hypophthalmichthys nobilis and Dorosoma cepedianum was more thoroughly described and illustrated than previous work with traditional microscopy techniques. The three-dimensional structure of gill rakers in Ictiobus cyprinellus was described and illustrated for the first time.

Journal of Fish Biology↗

USGS2006

Chlorophyll a and inorganic suspended solids in backwaters of the upper Mississippi River system: Backwater lake effects and their associations with selected environmental predictors

The Long Term Resource Monitoring Program (LTRMP) uses a stratified random sampling design to obtain water quality statistics within selected study reaches of the Upper Mississippi River System (UMRS). LTRMP sampling strata are based on aquatic area types generally found in large rivers (e.g., main channel, side channel, backwater, and impounded areas). For hydrologically well-mixed strata (i.e., main channel), variance associated with spatial scales smaller than the strata scale is a relatively minor issue for many water quality parameters. However, analysis of LTRMP water quality data has shown that within-strata variability at the strata scale is high in off-channel areas (i.e., backwaters). A portion of that variability may be associated with differences among individual backwater lakes (i.e., small and large backwater regions separated by channels) that cumulatively make up the backwater stratum. The objective of the statistical modeling presented here is to determine if differences among backwater lakes account for a large portion of the variance observed in the backwater stratum for selected parameters. If variance associated with backwater lakes is high, then inclusion of backwater lake effects within statistical models is warranted. Further, lakes themselves may represent natural experimental units where associations of interest to management may be estimated.

Open-File Report↗

USGS2025

Quantifying floodplain forest community change following large-scale flood events in the Upper Mississippi River System

Effects of large-scale flooding on forest composition and structure are a function of flood duration, depth, timing, and frequency. Throughout the Upper Mississippi River System (UMRS), floods in 1993 and 2019 were record-setting events followed by high rates of tree mortality. These events generated interest in species adaptations to flood event characteristics and how forest communities have changed in response to large-scale floods. We investigated associated tree mortality, how the floods differed spatially, and how floodplain forest communities have changed since 1993. Eight UMRS reaches were surveyed in a 1995 study, documenting vegetation species composition, size, and abundance. In 2021, a selection of plots (63%) were revisited and surveyed to quantify 2019 flood effects. For each site, we extracted daily inundation data for flood years and preceding decades from a surface water inundation model. We found post-flood mortality varied spatially and generally reflected inundation duration patterns. Lower latitude reaches experienced longer inundation durations and greater tree mortality in 1993 than in 2019, while higher latitude reaches experienced similar inundation duration and depth and similar mortality between events. Decadal inundation attributes also differed. During 2009–2018, inundation duration was greater and events occurred later than during 1983–1992 in all reaches. Most forest trajectories were Acer saccharinum -dominated and changed relatively little in species composition and structure. The greatest change in composition occurred at plots with high mortality from the 1993 flood, particularly in more flood-prone locations or where there were many small-diameter individuals. In plots dominated by either Quercus spp. or Populus deltoides , species importance shifted toward more shade and flood-tolerant species after 1995 surveys. Self-replacement of these species may be limited by a change in regeneration conditions resulting from an ongoing inundation regime shift in the case of Quercus spp., or succession to more shade-tolerant species in the case of Populus communities. Overall, effects on floodplain forests from the two flood events were heterogeneous. In some cases, forest change was likely just as influenced by shifts in flood regime as it was from singular flood events.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

USGS2009

Mercury concentrations and loads in a large river system tributary to San Francisco Bay, California, USA

In order to estimate total mercury (Hg T ) loads entering San Francisco Bay, USA, via the Sacramento-San Joaquin River system, unfiltered water samples were collected between January 2002 and January 2006 during high flow events and analyzed for Hg T . Unfiltered Hg T concentrations ranged from 3.2 to 75 ng/L and showed a strong correlation (r 2 = 0.8, p < 0.001, n = 78) to suspended sediment concentrations (SSC). During infrequent large floods, Hg T concentrations relative to SSC were approximately twice as high as observed during smaller floods. This difference indicates the transport of more Hg-contaminated particles during high discharge events. Daily Hg T loads in the Sacramento-San Joaquin River at Mallard Island ranged from below the limit of detection to 35 kg. Annual Hg T loads varied from 61 ?? 22 kg (n = 5) in water year (WY) 2002 to 470 ?? 170 kg (n = 25) in WY 2006. The data collected will assist in understanding the long-term recovery of San Francisco Bay from Hg contamination and in implementing the Hg total maximum daily load, the long-term cleanup plan for Hg in the Bay. ?? 2009 SETAC.

Environmental Toxicology and Chemistry↗

USGS2016

Telemetry narrows the search for sea lamprey spawning locations in the St. Clair-Detroit River System

Adult sea lamprey ( Petromyzon marinus ) abundance in Lake Erie has remained above targets set by fishery managers since 2005, possibly due to increased recruitment in the St. Clair-Detroit River System (SCDRS). Sea lamprey recruitment in the SCDRS poses an enormous challenge to sea lamprey control and assessment in Lake Erie because the SCDRS contains no dams to facilitate capture and discharge is at least an order of magnitude larger in the SCDRS than most other sea lamprey-producing tributaries in the Great Lakes. As a first step toward understanding population size, spatial distribution, and spawning habitat of adult sea lampreys in the SCDRS, we used acoustic telemetry to determine where sea lampreys ceased migration (due to spawning, death, or both) among major regions of the SCDRS. All tagged sea lampreys released in the lower Detroit River ( N = 27) moved upstream through the Detroit River and entered Lake St. Clair. After entering Lake St. Clair, sea lampreys entered the St. Clair River ( N = 22), Thames River ( N = 1), or were not detected again ( N = 4). Many sea lampreys (10 of 27) were last observed moving downstream (“fallback”) but we were unable to determine if those movements occurred before or after spawning, or while sea lampreys were dead or alive. Regardless of whether estimates of locations where sea lampreys ceased migration were based on the most upstream region occupied or final region occupied, most sea lampreys ceased migration in the St. Clair River or Lake St. Clair. Results suggest that spawning and rearing in the St. Clair River could be an important determinant of sea lamprey recruitment in the SCDRS and may direct future assessment and control activities in that system.

Michigan, Ontario↗