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USGS2025

How accurately does eDNA reflect the spatial distribution of cold-water fish? Field validation from a temperate lake

Applications of environmental DNA (eDNA) based detection technology to evaluate the distribution of aquatic organisms are increasing; yet field validations of eDNA are important to measure accuracy in study systems. To successfully apply this technology to species conservation, it is critical to understand how both species biology and environmental conditions affect the accuracy of inference from eDNA detection data. We implemented a field assessment of the accuracy and spatial resolution of eDNA-based species distributions for a native cold-water, schooling fish, cisco Coregonus artedi , that has been reintroduced to a deep temperate lake. We leveraged a combination of acoustic telemetry, providing known spatial locations of tagged fish, and lake-wide eDNA sampling to infer their distribution in Keuka Lake, New York, USA. Sub-surface (12 m and 18 m depths) eDNA samples were collected to accommodate the diel vertical migration behaviour of this fish species. The results of this study validated the accuracy of positive eDNA detections with the distribution of tagged fish to coarse spatial scales. Yet, several fine-scale locations revealed a mismatch between eDNA and acoustic telemetry detections; consistent with rapid transport of genetic material via lake currents. Empirical measurements of lake currents using drifters found cisco eDNA detections could deviate from specimens' source locations by as much as 3.3 km at 12 m depth or 1.5 km at 18 m depth over a 24 h transport period. Our study indicates that accurate species distributions estimated from eDNA sampling in lakes may require further understanding of transport mechanisms and persistence of environmental genetic material to relate point detections to source animal locations. Integrating eDNA sampling with additional data collection of species biology and environmental conditions will increase the spatial resolution of fish distribution assessments.

New York↗

USGS2010

Seasonal and interannual effects of hypoxia on fish habitat quality in central Lake Erie

1. Hypoxia occurs seasonally in many stratified coastal marine and freshwater ecosystems when bottom dissolved oxygen (DO) concentrations are depleted below 2–3 mg O 2 L -1 . 2. We evaluated the effects of hypoxia on fish habitat quality in the central basin of Lake Erie from 1987 to 2005, using bioenergetic growth rate potential (GRP) as a proxy for habitat quality. We compared the effect of hypoxia on habitat quality of (i) rainbow smelt, Osmerus mordax mordax Mitchill (young-of-year, YOY, and adult), a cold-water planktivore, (ii) emerald shiner, Notropis atherinoides Rafinesque (adult), a warm-water planktivore, (iii) yellow perch, Perca flavescens Mitchill (YOY and adult), a cool-water benthopelagic omnivore and (iv) round goby Neogobius melanostomus Pallas (adult) a eurythermal benthivore. Annual thermal and DO profiles were generated from 1D thermal and DO hydrodynamics models developed for Lake Erie’s central basin. 3. Hypoxia occurred annually, typically from mid-July to mid-October, which spatially and temporally overlaps with otherwise high benthic habitat quality. Hypoxia reduced the habitat quality across fish species and life stages, but the magnitude of the reduction varied both among and within species because of the differences in tolerance to low DO levels and warm-water temperatures. 4. Across years, trends in habitat quality mirrored trends in phosphorus concentration and water column oxygen demand in central Lake Erie. The per cent reduction in habitat quality owing to hypoxia was greatest for adult rainbow smelt and round goby (mean: -35%), followed by adult emerald shiner (mean: -12%), YOY rainbow smelt (mean: -10%) and YOY and adult yellow perch (mean: -8.5%). 5. Our results highlight the importance of differential spatiotemporally interactive effects of DO and temperature on relative fish habitat quality and quantity. These effects have the potential to influence the performance of individual fish species as well as population dynamics, trophic interactions and fish community structure.

Lake Erie↗

USGS2010

Do larval fishes exhibit diel drift patterns in a large, turbid river?

Previous research suggested larval fishes do not exhibit a diel drift cycle in turbid rivers (transparency <30 cm). We evaluated this hypothesis in the turbid, lower Missouri River, Missouri. We also reviewed diel patterns of larval drift over a range of transparencies in rivers worldwide. Larval fishes were collected from the Missouri River primary channel every 4 h per 24-h period during spring-summer 2002. Water transparency was measured during this period and summarized for previous years. Diel drift patterns were analyzed at the assemblage level and lower taxonomic levels for abundant groups. Day and night larval fish catch-per-unit-effort (CPUE) was compared for the entire May through August sampling period and spring (May - June) and summer (July - August) seasons separately. There were no significant differences between day and night CPUE at the assemblage level for the entire sampling period or for the spring and summer seasons. However, Hiodon alosoides, Carpiodes/Ictiobus spp. and Macrhybopsis spp. exhibited a diel cycle of abundance within the drift. This pattern was evident although mean Secchi depth (transparency) ranged from 4 to 25 cm during the study and was <30 cm from May through August over the previous nine years. Larval diel drift studies from 48 rivers excluding the Missouri River indicated the primary drift period for larval fishes was at night in 38 rivers and during the day for five, with the remaining rivers showing no pattern. Water transparency was reported for 10 rivers with six being <30 cm or 'low'. Two of these six turbid rivers exhibited significant diel drift patterns. The effect of water transparency on diel drift of larval fishes appears taxa-specific and patterns of abundant taxa could mask patterns of rare taxa when analyzed only at the assemblage level. ?? 2010 Blackwell Verlag, Berlin.

Journal of Applied Ichthyology↗

USGS2018

Potential responses of the Lower Missouri River Shovelnose Sturgeon (Scaphirhynchus platorynchus) population to a commercial fishing ban

We developed an age‐structured population matrix model to perform population viability analysis for Lower Missouri River (LMR) shovelnose sturgeon ( Scaphirhynchus platorynchus ). We investigated potential effects of the commercial fishing moratorium put in place to help protect the similar‐appearing pallid sturgeon ( S. albus ). The model applies different components of total variance in life history parameters at different levels: sampling variance (parameter uncertainty) between model iterations; temporal variance (temporal environmental fluctuations) between time steps within iterations; and individual variance (individual differences) within each time‐step. The model predicted annual rates of population increase of 1.96% under historic fishing and 2.67% with removal of historic fishing. We identified combinations of fishing and harvest size restrictions that would permit a sustainable harvest of shovelnose sturgeon. Overall, the ban on commercial fishing of shovelnose sturgeon in the LMR due to similarity of appearance to pallid sturgeon should help the LMR shovelnose sturgeon population begin to rebound while decreasing any negative effects it may have had on pallid sturgeon populations.

Lower Missouri River basin↗

USGS2012

Nutrient enrichment and fish nutrient tolerance: Assessing biologically relevant nutrient criteria

Relationships between nutrient concentrations and fish nutrient tolerance were assessed relative to established nutrient criteria. Fish community, nitrate plus nitrite (nitrate), and total phosphorus (TP) data were collected during summer low-flow periods in 2003 and 2004 at stream sites along a nutrient-enrichment gradient in an agricultural basin in Indiana and Ohio and an urban basin in the Atlanta, Georgia, area. Tolerance indicator values for nitrate and TP were assigned for each species and averaged separately for fish communities at each site (TIV o ). Models were used to predict fish species expected to occur at a site under minimally disturbed conditions and average tolerance indicator values were determined for nitrate and TP separately for expected communities (TIV e ). In both areas, tolerance scores (TIV o /TIV e ) for nitrate increased significantly with increased nitrate concentrations whereas no significant relationships were detected between TP tolerance scores and TP concentrations. A 0% increase in the tolerance score (TIV o /TIV e = 1) for nitrate corresponded to a nitrate concentration of 0.19 mg/l (compared with a USEPA summer nitrate criterion of 0.17 mg/l) in the urban area and 0.31 mg/l (compared with a USEPA summer nitrate criterion of 0.86 mg/l) in the agricultural area. Fish nutrient tolerance values offer the ability to evaluate nutrient enrichment based on a quantitative approach that can provide insights into biologically relevant nutrient criteria.

Georgia, Indiana, Ohio↗

USGS2020

Using Markov chains to quantitatively assess movement patterns of invasive fishes impacted by a carbon dioxide barrier in outdoor ponds

Natural resource managers use barriers to deter the movement of aquatic invasive species. Research and development of new invasive species barriers is often evaluated in pond and field scales using high‐resolution telemetry data. Telemetry data sets can be a rich source of data about fish movement and behavior but can be difficult to analyze due to the size of these data sets as well as their irregular sampling intervals. Due to the challenges, most barrier studies only use summary endpoints, such as barrier passage counts or average (e.g., mean or median) fish distance from the barrier, to describe the data. To examine more fine‐scale fish movement patterns, we developed a first‐order Markov chain. We then used this model to help understand the impacts of a barrier on fish behavior. For our study system, we used data from a previous study examining how bighead and silver carp (two invasive fish species in the United States) responded to a carbon dioxide (CO 2 ) barrier in a pond.

Natural Resource Modeling↗

USGS1973

Fish viruses: Buffers and methods for plaquing eight agents under normal atmosphere

A universal procedure was sought for plaque assay of eight fish viruses (bluegill myxovirus, channel catfish virus, eel virus, Egtved virus, infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus, lymphocystis virus, and the agent of spring viremia of carp ( Rhabdovirus carpio ), in dish cultures of various fish cells. Eagle minimal essential medium with sodium bicarbonate-CO 2 buffer (Earle’s salt solution) was compared with minimal essential medium buffered principally with tris (hydroxymethyl)aminomethane or N -2-hydroxyethylpiperazine-N′-2′-ethanesulfonic acid at a pH or in the range of 7.6 to 8.0 depending upon temperature. Five fish cell lines collectively capable of replicating all fish viruses thus far isolated were tested and quantitatively found to grow comparably well in the three media. Two-phase (gel-liquid) media incorporating the various buffer systems allowed plaquing at 15 to 33 C either in partial pressures of CO 2 or in normal atmosphere, but greater efficiency and sensitivity were obtained with the organic buffers, and, overall, the best results were obtained with tris(hydroxymethyl)aminomethane. Epizootiological data, specific fish cell line response, and plaque morphology permit presumptive identification of most of the agents. At proper pH, use of organic buffers obviates the need for CO 2 incubators.

Applied Microbiology↗

USGS1952

Glaciation and drainage changes in the fish Lake Plateau, Utah

The Fish Lake Plateau , nearly centrally located among the High Plateaus of Utah , exhibits glacial and other geomorphic features of regional significance. The plateau is divided into two areas by Fish Lake and the wide valley of Sevenmile Creek. The Fish Lake trough is a structural basin; Sevenmile Valley may be largely erosional. Volcanic rocks of Tertiary age underlie most of the plateau ; early Tertiary sedimentary rocks are also present. Glaciated canyons with well-developed cirques are especially prominent along the east-facing sides of the Fish Lake trough and Sevenmile Valley. Ice-eroded features occur over much of the plateau top. Near the mouths of several of the glaciated canyons are two conspicuous sets of moraines. The older set is more extensive and less rugged than the younger and occurs at somewhat lower elevations. Two substages of glaciation thus recognized are correlated with Wisconsin I and II of Ray; probable correlatives of Wisconsin III, IV, and V are represented by moraines which are younger than these two sets. Fish Lake drains north into Fremont River, a tributary of the Colorado River. An abandoned southern outlet and waterfall, the latter at a higher elevation than the present elevation of the original northern bedrock divide, indicate drainage reversal. Evidence is presented which suggests that this reversal was pre-glacial and probably the result of fault-block tilting.

Utah↗

USGS2015

Coupling age-structured stock assessment and fish bioenergetics models: a system of time-varying models for quantifying piscivory patterns during the rapid trophic shift in the main basin of Lake Huron

We quantified piscivory patterns in the main basin of Lake Huron during 1984–2010 and found that the biomass transfer from prey fish to piscivores remained consistently high despite the rapid major trophic shift in the food webs. We coupled age-structured stock assessment models and fish bioenergetics models for lake trout ( Salvelinus namaycush ), Chinook salmon ( Oncorhynchus tshawytscha ), walleye ( Sander vitreus ), and lake whitefish ( Coregonus clupeaformis ). The model system also included time-varying parameters or variables of growth, length–mass relations, maturity schedules, energy density, and diets. These time-varying models reflected the dynamic connections that a fish cohort responded to year-to-year ecosystem changes at different ages and body sizes. We found that the ratio of annual predation by lake trout, Chinook salmon, and walleye combined with the biomass indices of age-1 and older alewives ( Alosa pseudoharengus ) and rainbow smelt ( Osmerus mordax ) increased more than tenfold during 1987–2010, and such increases in predation pressure were structured by relatively stable biomass of the three piscivores and stepwise declines in the biomass of alewives and rainbow smelt. The piscivore stability was supported by the use of alternative energy pathways and changes in relative composition of the three piscivores. In addition, lake whitefish became a new piscivore by feeding on round goby ( Neogobius melanostomus ). Their total fish consumption rivaled that of the other piscivores combined, although fish were still a modest proportion of their diet. Overall, the use of alternative energy pathways by piscivores allowed the increases in predation pressure on dominant diet species.

Lake Huron↗

USGS2018

Sampling the stream landscape: Improving the applicability of an ecoregion-level capture probability model for stream fishes

Temporal and spatial variability in streams result in heterogeneous gear capture probability (i.e., the proportion of available individuals identified) that confounds interpretation of data used to monitor fish abundance. We modeled tow-barge electrofishing capture probability at multiple spatial scales for nine Ozark Highland stream fishes. In addition to fish size, we identified seven reach-scale environmental characteristics associated with variable capture probability: stream discharge, water depth, conductivity, water clarity, emergent vegetation, wetted width–depth ratio, and proportion of riffle habitat. The magnitude of the relationship between capture probability and both discharge and depth varied among stream fishes. We also identified lithological characteristics among stream segments as a coarse-scale source of variable capture probability. The resulting capture probability model can be used to adjust catch data and derive reach-scale absolute abundance estimates across a wide range of sampling conditions with similar effort as used in more traditional fisheries surveys (i.e., catch per unit effort). Adjusting catch data based on variable capture probability improves the comparability of data sets, thus promoting both well-informed conservation and management decisions and advances in stream-fish ecology.

Arkansas, Missouri, Oklahoma↗

USGS2019

Probabilistic relationships between acid-base chemistry and fish assemblages in streams of the western Adirondack Mountains, New York, USA

Surface waters across much of the Adirondacks of New York were acidified in the late 20th century but began to recover after the 1990 amendments to the Clean Air Act. Little data, however, were available to characterize biological impacts and predict recovery of fish assemblages in regional streams. Quantitative fish and chemistry surveys were completed in 47 headwater streams during summer 2014-16 to develop logistic (probabilistic) models that characterize the status of contemporary fish assemblages and predict how different N and S deposition loads may affect future fish assemblages. Models for Ali and richness ≥1 species, ANC and total density >400 fish/0.1 ha, ANC and total biomass >1500 g/0.1, presence of Brook Trout, trout density >200 fish/0.1 ha, and trout biomass >1000 g/0.1 ha were suitable for evaluating community and population responses to changes in acid-base chemistry. Anticipated changes in national (US) secondary standards for atmospheric emissions of NOx and SOx to achieve target N and S deposition loads will alter acid-base chemistry and the probabilities for observing various levels of fish metrics in streams across the region and elsewhere.

New York↗

USGS2019

Predicting fish species richness and habitat relationships using Bayesian hierarchical multispecies occupancy models

Understanding how stream fishes respond to changes in habitat availability is complicated by low occurrence rates of many species, which in turn reduces the ability to quantify species–habitat relationships and account for imperfect detection in estimates of species richness. Multispecies occupancy models have been used sparingly in the analysis of fisheries data, but address the aforementioned deficiencies by allowing information to be shared among ecologically similar species, thereby enabling species–habitat relationships to be estimated for entire fish communities, including rare species. Here, we highlight the utility of hierarchical multispecies occupancy models for the analysis of fish community data and demonstrate the modeling framework on a stream fish community dataset collected in the Delaware Water Gap National Recreation Area, USA. In particular, we demonstrate the ability of the modeling framework to make inferences at the species-, guild-, and community-levels, thereby making it a powerful tool for understanding and predicting how environmental variables influence species occupancy probabilities and structure fish assemblages.

New York New Jersey, Pennsylvania↗

USGS2021

A framework for assessing the ability to detect macroscale effects on fish growth

Various abiotic and biotic factors affect fish and their habitats at macroscales. For example, changes in global temperatures will likely alter demographic rates, including growth. However, to date, there is no statistical framework for assessing the ability to detect macroscale effects on fish growth under different sampling scenarios. We provide a generalized framework for calculating the frequentist and Bayesian power of detecting macroscale effects on fish growth. We illustrate this framework for a range of sampling scenarios that varied in the number of fish sampled per lake, the number of lakes sampled, and the magnitude of the temperature effect on growth for two case study species. However, the framework can be adapted to investigate other species, sampling scenarios, and environmental drivers. The ability to detect macroscale effects was more affected by the number of lakes sampled rather than the number of fish sampled from each lake. Confidently detecting macroscale effects likely requires sampling hundreds of lakes. This was true for both case study species, despite different life histories and extents of spatial variability in growth.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2023

The scale-dependent role of submerged macrophytes as drift-feeding lotic fish habitat

Although submerged macrophyte (hereafter, “macrophyte”) communities are globally prevalent in low-gradient rivers, the net reach-scale effect of macrophytes on drift-feeding fish microhabitat preference is poorly understood. We used snorkeling and bioenergetics to study fish habitat selection for rainbow trout ( Oncorhynchus mykiss ) in the Henrys Fork, ID, USA, investigating microhabitat preference across a reach-scale gradient of macrophyte growth. Fish preferred microhabitats with deep water, low velocity, and low macrophyte coverage. Preferences for microhabitats with higher net rate of energy intake (NREI) were modulated by reach-scale macrophyte coverage, higher coverage increasing preferences for higher NREI. Macrophyte coverage was a weak positive predictor for depth and NREI, and a weak negative predictor for water velocity and median substrate. Our results suggest trade-offs between fish predation risk and bioenergetic food intake, with macrophytes modulating these trade-offs across scales by affecting reach-scale geomorphology, bioenergetics, and predation risk. As such, this study highlights the important and dynamic role that macrophytes can play in fish population dynamics in rivers, with important implications for management decisions.

Idaho↗

USGS2024

Paired comparisons with quiet surface drones show evidence of fish behavioral response to motorized vessels during acoustic surveys in Lake Superior

Acoustic surveys are important for fish stock assessments, but fish responses to survey vessels can bias acoustic estimates. We leveraged quiet uncrewed surface vessels (USVs) to characterize potential bias in acoustic surveys. Five conventional motorized ships overtook USVs from astern over 2 km transects at night in Lake Superior in 2022. We examined the difference in acoustic backscatter, average target depth, and average target strength (TS) between USV and motorized vessels. Although sound level measurements from the motorized vessels sometimes exceeded recommendations for scientific vessels, we did not detect differences in acoustic measures among survey vessels. However, the USVs recorded 2 dB higher acoustic backscatter and TS than motorized vessels, leading to ~15% higher fish densities with drones when using in situ TS and echo integration. Differences in fish density would increase to 30-60% if a standard TS value was applied. Target depth did not differ between USVs and motorized ships. These results are consistent with a change in orientation but not depth of insonified fish and limited horizontal avoidance of motorized survey vessels.

Lake Superior↗

USGS2026

Identifying overlap between native fish movements and a possible seasonal Grass Carp deterrent in the Sandusky River, Ohio, USA

Riverine fishes are vulnerable to habitat fragmentation caused by interrupted access to vital habitats. Fragmentation using artificial structures can be used to limit the spread of invasive fishes by inhibiting movement between critical habitats. Thus, tradeoffs exist between maintaining connectivity for native species and restricting movement of invasive fishes. A nonphysical deterrent has been proposed to prevent invasive Grass Carp ( Ctenopharyngodon idella ) from reaching spawning habitats in the Sandusky River, a tributary to Lake Erie, during late spring–summer. However, this timing overlaps with spawning periods of a suite of native fishes. We used acoustic telemetry and ichthyoplankton surveys to examine movement and spawning activity of multiple native species and to assess potential impacts of deterrent operation on reproduction. All species used the proposed deterrent location during the Grass Carp spawning period, and their movements corresponded with larval fish collections, indicating upstream spawning. These findings suggest the deterrent could unintentionally restrict native species’ access to essential habitats. Balancing habitat connectivity and invasive species control will likely depend on species-specific responses and careful timing of deterrent operation.

Ohio↗

USGS2003

Fish community change in Lake Superior, 1970-2000

Changes in Lake Superior's fish community are reviewed from 1970 to 2000. Lake trout ( Salvelinus namaycush ) and lake whitefish ( Coregonus clupeaformis ) stocks have increased substantially and may be approaching ancestral states. Lake herring ( Coregonus artedi ) have also recovered, but under sporadic recruitment. Contaminant levels have declined and are in equilibrium with inputs, but toxaphene levels are higher than in all other Great Lakes. Sea lamprey ( Petromyzon marinus ) control, harvest limits, and stocking fostered recoveries of lake trout and allowed establishment of small nonnative salmonine populations. Natural reproduction supports most salmonine populations, therefore further stocking is not required. Nonnative salmonines will likely remain minor components of the fish community. Forage biomass has shifted from exotic rainbow smelt ( Osmerus mordax ) to native species, and high predation may prevent their recovery. Introductions of exotics have increased and threaten the recovering fish community. Agencies have little influence on the abundance of forage fish or the major predator, siscowet lake trout, and must now focus on habitat protection and enhancement in nearshore areas and prevent additional species introductions to further restoration. Persistence of Lake Superior's native deepwater species is in contrast to other Great Lakes where restoration will be difficult in the absence of these ecologically important fishes.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2010

Environmental drivers of fish functional diversity and composition in the Lower Colorado River Basin

Freshwater conservation efforts require an understanding of how natural and anthropogenic factors shape the present-day biogeography of native and non-native species. This knowledge need is especially acute for imperiled native fishes in the highly modified Lower Colorado River Basin (LCRB), USA. In the present study we employed both a taxonomic and functional approach to explore how natural and human-related environmental drivers shape landscape-scale patterns of fish community composition in the LCRB. Our results showed that hydrologic alteration, watershed land use, and regional climate explained 30.3% and 44.7% of the total variation in fish community taxonomic and functional composition, respectively. Watersheds with greater dam densities and upstream storage capacity supported higher non-native functional diversity, suggesting that dams have provided additional "niche opportunities" for non-native equilibrium life-history strategists by introducing new reservoir habitat and modifying downstream flow and thermal regimes. By contrast, watersheds characterized by greater upstream land protection, lower dam densities, and higher variation in spring and summer precipitation supported fish communities with a strong complement of native species (opportunistic-periodic strategists). In conclusion, our study highlights the utility of a life-history approach to better understand the patterns and processes by which fish communities vary along environmental gradients.

Canadian Journal of Fisheries and Aquatic Sciences↗