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USGS2024

Lake temperature and morphometry shape the thermal composition of recreational fishing catch

Objective Managing freshwater fisheries in warming lakes is challenging because climate change impacts anglers, fish, and their interactions. Methods We integrated recent models of current and future lake temperatures with recreational fisheries catch data from 587 lakes in three north-central U.S. states (Michigan, Minnesota, and Wisconsin) to evaluate how the thermal composition of recreational fisheries catch varied as a function of temperature, ice coverage, and lake morphometry. Result We found that warmwater catch share (WCS), defined as the proportion of fish in recreational angling catch that belonged to the warmwater thermal guild (final temperature preferendum [FTP] > 25°C), increased with average annual lake surface temperature and decreased with survey ice coverage. However, we also found that WCS decreased with increased lake area and depth. Using mid-century (2040–2060) water temperature and ice projections while holding all other variables constant, we predicted that WCS will likely increase as the climate warms but that significant thermal heterogeneity will persist. Conclusion Lakes that are large (>100 ha) and deep (>10 m) and those with cooler (<3700 annual growing degree-days) predicted future temperatures will likely hold thermal refugia for coolwater (FTP = 19–25°C) and coldwater (FTP < 19°C) fish even as average lake temperatures rise, creating the potential for management actions to resist the shift from coolwater to warmwater fisheries. Managers of smaller and more rapidly warming lakes may want to consider strategies that accept or direct emerging warmwater fishing opportunities. We suggest that the most viable path to climate adaptation in landscapes of diverse lakes may be to resist warmwater shifts where possible and to accept or direct the rise of warmwater fishing opportunities where necessary.

Michigan, Minnesota, Wisconsin↗

USGS1999

Fishes in mangrove prop-root habitats of northeastern Florida Bay: Distinct assemblages across an estuarine gradient

Seasonal changes in freshwater inflow and other environmental conditions may induce changes in density and species composition of mangrove fishes along estuarine gradients. Fishes within mangrove habitats in a subtropical estuary were sampled monthly from May 1989 to May 1990, using block nets with rotenone and visual censuses. At 18 stations, temperature ranged from 22 to 34°C, depth from 10 to 104cm and underwater visibility from 1 to 13m. Salinity ranged from 0 to 60 upstream, and 35 to 54 mid- and downstream. A total of 573191 individuals (76 species) was observed or collected, with an average density of 6·5 fish m −2 . Engraulidae, Atherinidae, Poeciliidae and Cyprinodontidae numerically dominated the assemblage. Distinct assemblages occurred up-, mid- and downstream and maintained coherent groups in these gradient positions over the seasons. Residents totalled 94·5% of the individuals, estuarine transients comprised 5·1% and occasional marine visitors were less than 0·4%. Densities of resident fishes peaked in winter as temperatures and water levels fell, uncorrelated with changes in salinity. These observations suggest that mangrove habitats may sustain diverse and abundant fish communities dominated by euryhaline residents. Although estuarine transients were consistently rare in upstream sub-basins, downstream were found numerous sub-adults of species occurring as adults on nearby reefs (Lutjanidae, Haemulidae). Thus, reef-associated estuarine transients may be abundant in mangrove habitats having near-marine salinities. Contrary to expectations, mangrove habitats in northeastern Florida bay did not function as a nursery as defined under the nursery-ground paradigm: young-of-the-year juveniles of estuarine transient species did not seek low salinity sub-basins. However, northeastern Florida Bay may not be representative of most mangrove estuaries as the area: (1) is without lunar tides and related circulation; (2) has low and variable amounts of submersed vegetation; and (3) experiences severe hypersaline conditions.

Estuarine, Coastal and Shelf Science↗

USGS2017

Fish remains from Homestead Cave and lake levels of the past 13,000 years in the Bonneville basin

A late Quaternary ichthyofauna from Homestead Cave, Utah, provides a new source of information on lake history in the Bonneville basin. The fish, represented by 11 freshwater species, were accumulated between ~11,200 and ~1000 14C yr B.P. by scavenging owls. The 87Sr/86Sr ratio of Lake Bonneville varied with its elevation; 87Sr/86Sr values of fish from the lowest stratum of the cave suggest they grew in a lake near the terminal Pleistocene Gilbert shoreline. In the lowest deposits, a decrease in fish size and an increase in species tolerant of higher salinities or temperatures suggest multiple die-offs associated with declining lake levels. An initial, catastrophic, post-Provo die-off occurred at 11,300-11,200 14C yr B.P. and was followed by at least one rebound or recolonization of fish populations, but fish were gone from Lake Bonneville sometime before ~10,400 14C yr B.P. This evidence is inconsistent with previous inferences of a near desiccation of Lake Bonneville between 13,000 and 12,000 14C yr B.P. Peaks in Gila atraria frequencies in the upper strata suggest the Great Salt Lake had highstands at ~3400 and ~1000 14C yr B.P. (C) 2000 University of Washington.

Quaternary Research↗

USGS2023

Aging contrast: A contrastive learning framework for fish re-identification across seasons and years.

The fields of biology, ecology, and fisheries management are witnessing a growing demand for distinguishing individual fish. In recent years, deep learning methods have emerged as a promising tool for image-based fish recognition. Our study is focused on the re-identification of masu salmon from Japan, wherein fish were individually marked and photographed to evaluate discriminative body characteristics. Unlike previous studies where fish were sampled during the same time period, we evaluated individual re-identification across seasons and years to address challenges due to aging, seasonal variation, and other factors. In this paper, we propose a new contrastive learning framework called Ag ing Co ntrast (AgCo) and evaluate its performance on the masu salmon dataset. Our analysis indicates that, unlike large changes in body size over time, the pattern of parr marks on the lateral line of the fish body remains relatively stable, despite some change in coloration across seasons. AgCo accounts for such seasonally-invariant features and performs re-identification based on the cosine similarity of these features. Extensive experiments show that our AgCo method outperforms other state-of-the-art methods.

Conference Paper↗

USGS2005

Concentrations of cadmium, lead, and zinc in fish from mining-influenced waters of northeastern Oklahoma: Sampling of blood, carcass, and liver for aquatic biomonitoring

The Tri-States Mining District (TSMD) of Missouri (MO), Kansas (KS), and Oklahoma (OK), USA, was mined for lead (Pb) and zinc (Zn) for more than a century. Mining ceased more than 30 years ago, but wastes remain widely distributed in the region, and there is evidence of surface- and groundwater contamination in the Spring River-Neosho River (SR-NR) system of northeastern OK. In October 2001, we collected a total of 74 fish from six locations in the SR-NR system that included common carp (Cyprinus carpio), channel- and flathead catfish (Ictalurus punctatus and Pylodictis olivaris), largemouth- and spotted bass (Micropterus salmoides and Micropterus punctulatus), and white crappie (Pomoxis annularis). We obtained additional fish from locations in MO that included three reference sites and one site that served as a "positive control" (heavily contaminated by Pb). Blood, carcass (headed, eviscerated, and scaled) and liver (carp only) samples were analyzed for cadmium (Cd), Pb, and Zn. Our objectives were to assess the degree to which fish from the OK portion of the SR-NR system are contaminated by these elements and to evaluate fish blood sampling for biomonitoring. Concentrations of Cd and Pb in carp and catfish from OK sites were elevated and Pb concentrations of some approached those of the highly contaminated site in MO, but concentrations in bass and crappie were relatively low. For Zn, correlations were weak among concentrations in the three tissues and none of the samples appeared to reflect site contamination. Variability was high for Cd in all three tissues of carp; differences between sites were statistically significant (p < 0.05) only for blood even though mean liver concentrations were at least 100-fold greater than those in blood. Blood concentrations of Cd and Pb were positively correlated (r 2 = 0.49 to 0.84) with the concentration of the same element in carp and catfish carcasses or in carp livers, and the corresponding multiple regression models were highly significant (p < 0.001). Our data indicate that potentially nonlethal blood sampling can be useful for monitoring of selected metals in carp, catfish, and perhaps other fishes. ?? 2005 Springer Science+Business Media, Inc.

Archives of Environmental Contamination and Toxico↗

USGS2007

Concentrations of metals in water, sediment, biofilm, benthic macroinvertebrates, and fish in the Boulder River watershed, Montana, and the role of colloids in metal uptake

To characterize the partitioning of metals in a stream ecosystem, concentrations of trace metals including As, Cd, Cu, Pb, and Zn were measured in water, colloids, sediment, biofilm (also referred to as aufwuchs ), macroinvertebrates, and fish collected from the Boulder River watershed, Montana. Median concentrations of Cd, Cu, and Zn in water throughout the watershed exceeded the U.S. EPA acute and chronic criteria for protection of aquatic life. Concentrations of As, Cd, Cu, Pb, and Zn in sediment were sufficient in the tributaries to cause invertebrate toxicity. The concentrations of As, Cu, Cd, Pb, and Zn in invertebrates from lower Cataract Creek (63, 339, 59, 34, and 2,410 μg/g dry wt, respectively) were greater than the concentrations in invertebrates from the Clark Fork River watershed, Montana (19, 174, 2.3, 15, and 648 μg/g, respectively), that were associated with reduced survival, growth, and health of cutthroat trout fed diets composed of those invertebrates. Colloids and biofilm seem to play a critical role in the pathway of metals into the food chain and concentrations of As, Cu, Pb, and Zn in these two components are significantly correlated. We suggest that transfer of metals associated with Fe colloids to biological components of biofilm is an important pathway where metals associated with abiotic components are first available to biotic components. The significant correlations suggest that Cd, Cu, and Zn may move independently to biota (biofilm, invertebrates, or fish tissues) from water and sediment. The possibility exists that Cd, Cu, and Zn concentrations increase in fish tissues as a result of direct contact with water and sediment and indirect exposure through the food chain. However, uptake through the food chain to fish may be more important for As. Although As concentrations in colloids and biofilm were significantly correlated with As water concentrations, As concentrations in fish tissues were not correlated with water. The pathway for Pb into biological components seems to begin with sediment because concentrations of Pb in water were not significantly correlated with any other component and because concentrations of Pb in the water were often below detection limits.

Montana↗

USGS2014

Sustainability of the Lake Superior fish community: Interactions in a food web context

The restoration and rehabilitation of the native fish communities is a long-term goal for the Laurentian Great Lakes. In Lake Superior, the ongoing restoration of the native lake trout populations is now regarded as one of the major success stories in fisheries management. However, populations of the deepwater morphotype (siscowet lake trout) have increased much more substantially than those of the nearshore morphotype (lean lake trout), and the ecosystem now contains an assemblage of exotic species such as sea lamprey, rainbow smelt, and Pacific salmon (chinook, coho, and steelhead). Those species play an important role in defining the constraints and opportunities for ecosystem management. We combined an equilibrium mass balance model (Ecopath) with a dynamic food web model (Ecosim) to evaluate the ecological consequences of future alternative management strategies and the interaction of two different sets of life history characteristics for fishes at the top of the food web. Relatively rapid turnover rates occur among the exotic forage fish, rainbow smelt, and its primary predators, exotic Pacific salmonids. Slower turnover rates occur among the native lake trout and burbot and their primary prey—lake herring, smelt, deepwater cisco, and sculpins. The abundance of forage fish is a key constraint for all salmonids in Lake Superior. Smelt and Mysis play a prominent role in sustaining the current trophic structure. Competition between the native lake trout and the exotic salmonids is asymmetric. Reductions in the salmon population yield only a modest benefit for the stocks of lake trout, whereas increased fishing of lake trout produces substantial potential increases in the yields of Pacific salmon to recreational fisheries. The deepwater or siscowet morphotype of lake trout has become very abundant. Although it plays a major role in the structure of the food web it offers little potential for the restoration of a valuable commercial or recreational fishery. Even if a combination of strong management actions is implemented, the populations of lean (nearshore) lake trout cannot be restored to pre-fishery and pre-lamprey levels. Thus, management strategy must accept the ecological constraints due in part to the presence of exotics and choose alternatives that sustain public interest in the resources while continuing the gradual progress toward restoration.

Ecosystems↗

USGS2010

Abandoned mine drainage in the Swatara Creek Basin, southern anthracite coalfield, Pennsylvania, USA: 1. stream quality trends coinciding with the return of fish

Acidic mine drainage (AMD) from legacy anthracite mines has contaminated Swatara Creek in eastern Pennsylvania. Intermittently collected base-flow data for 1959–1986 indicate that fish were absent immediately downstream from the mined area where pH ranged from 3.5 to 7.2 and concentrations of sulfate, dissolved iron, and dissolved aluminum were as high as 250, 2.0, and 4.7 mg/L, respectively. However, in the 1990s, fish returned to upper Swatara Creek, coinciding with the implementation of AMD treatment (limestone drains, limestone diversion wells, limestone sand, constructed wetlands) in the watershed. During 1996–2006, as many as 25 species of fish were identified in the reach downstream from the mined area, with base-flow pH from 5.8 to 7.6 and concentrations of sulfate, dissolved iron, and dissolved aluminum as high as 120, 1.2, and 0.43 mg/L, respectively. Several of the fish taxa are intolerant of pollution and low pH, such as river chub (Nocomis icropogon) and longnose dace (Rhinichthys cataractae). Cold-water species such as brook trout (Salvelinus fontinalis) and warm-water species such as rock bass (Ambloplites rupestris) varied in predominance depending on stream flow and stream temperature. Storm flow data for 1996–2007 indicated pH, alkalinity, and sulfate concentrations decreased as the stream flow and associated storm-runoff component increased, whereas iron and other metal concentrations were poorly correlated with stream flow because of hysteresis effects (greater metal concentrations during rising stage than falling stage). Prior to 1999, pH\5.0 was recorded during several storm events; however, since the implementation of AMD treatments, pH has been maintained near neutral. Flow-adjusted trends for1997–2006 indicated significant increases in calcium; decreases in hydrogen ion, dissolved aluminum, dissolved and total manganese, and total iron; and no change in sulfate or dissolved iron in Swatara Creek immediately downstream from the mined area. The increased pH and calcium from limestone in treatment systems can be important for mitigating toxic effects of dissolved metals. Thus, treatment of AMD during the 1990s improved pH buffering, reduced metals transport, and helped to decrease metals toxicity to fish.

Pennsylvania↗

USGS2008

PCDDs, PCDFs, PCBs, OC pesticides and mercury in fish and osprey eggs from Willamette River, Oregon (1993, 2001 and 2006) with calculated biomagnification factors

The osprey (Pandion haliaetus) population nesting along the main stem Willamette River and lower Santiam River was first studied to evaluate contaminants and reproductive rates in 1993 when 78 occupied nests were present. By 2001, the population increased to 234 occupied nests, a 13.7% annual rate of population increase. A sample egg was collected from each of a series of nests along the Upper River (river mile 55-187) in 1993, 2001 and 2006 to evaluate trends of persistent contaminants (organochlorine [OC] pesticides, polychlorinated biphenyls [PCBs], polychlorinated dibenzo-p-dioxins [PCDDs], and polychlorinated dibenzofurans [PCDFs]). Nearly all OC pesticide residues decreased significantly, e.g., p, p?-DDE (DDE) from 2,350 to 1,353 to 210 ??g/kg wet weight (ww). PCBs followed a similar pattern over time, e.g., ???PCBs 688 to 245 to 182 ??g/kg ww, while PCDDs and PCDFs showed a more precipitous decline (often 85-95%) between 1993 and 2001, with no egg analyses warranted in 2006. During 2001-2002, sample osprey eggs were also collected from nests at three Headwater Reservoirs and two lower reaches (Newberg Pool and Tidal Portland) of the Willamette River, as well as the lower portion of the Santiam River to evaluate spatial residue patterns. Significant differences were seldom detected among the different sampling areas for OC pesticides (probably due to small sample sizes), although higher concentrations were often seen in the lower reaches, e.g., DDE 901 ??g/kg ww (Headwater Reservoirs), 1,353 (Upper River), 1,384 (Newberg Pool) and 2,676 (Tidal Portland). PCB congener concentrations in eggs were usually higher in the Tidal Portland reach than at other locations and often significantly higher than at the Headwater Reservoirs or Upper River. Mercury (first analyzed in eggs in 2001), PCDDs and PCDFs were extremely low in 2001/2002 with no significant spatial patterns. Whole fish composite samples of largescale sucker (Catastomus macrocheilus) and northern pikeminnow (Ptychocheilus oregonensis), which account for about 90% of the biomass in the diet of this osprey population, were also collected from the Willamette River in 1993 and 2001 and analyzed for the same contaminants as osprey eggs. Contaminant residues in fish from the Upper River decreased between 1993 and 2001, paralleling findings for osprey eggs. Likewise, spatial patterns for fish residues paralleled findings for osprey eggs from the different reaches in 2001. A second empirical estimate of biomagnification factors (BMFs) from fish to osprey eggs for OC pesticides, PCBs, PCDDs and PCDFs (ww and lipid weight [lw] basis) was calculated based on residue data collected in 2001. The two independent BMF estimates (1993 and 2001) for each contaminant from the Upper River provide a measure of consistency, e.g., DDE (ww) 87 and 79, (lw) 103 and 112; ???PCBs (ww) 11 and 8.4, (lw) 13 and 12. Mercury did not biomagnify from fish to osprey eggs (BMF = 0.60). Legacy contaminants investigated had limited (perhaps only DDE), if any, effects on reproductive success of the increasing osprey population nesting along the Willamette River by 2001. ?? 2008 U.S. Government.

Ecotoxicology↗

USGS2011

Spatial patterns of mercury in macroinvertebrates and fishes from streams of contrasting forested landscapes in the eastern United States

Controls on mercury bioaccumulation in lotic ecosystems are not well understood. During 2007–2009, we studied mercury and stable isotope spatial patterns of macroinvertebrates and fishes from two medium-sized (<80 km 2 ) forested basins in contrasting settings. Samples were collected seasonally from multiple sites across the Fishing Brook basin (FBNY), in New York's Adirondack Mountains, and the McTier Creek basin (MCSC), in South Carolina's Coastal Plain. Mean methylmercury (MeHg) concentrations within macroinvertebrate feeding groups, and mean total mercury (THg) concentrations within most fish feeding groups were similar between the two regions. However, mean THg concentrations in game fish and forage fish, overall, were much lower in FBNY (1300 and 590 ng/g dw, respectively) than in MCSC (2300 and 780 ng/g dw, respectively), due to lower trophic positions of these groups from FBNY (means 3.3 and 2.7, respectively) than MCSC (means 3.7 and 3.3, respectively). Much larger spatial variation in topography and water chemistry across FBNY contributed to greater spatial variation in biotic Hg and positive correlations with dissolved MeHg and organic carbon in streamwater. Hydrologic transport distance (HTD) was negatively correlated with biotic Hg across FBNY, and was a better predictor than wetland density. The small range of landscape conditions across MCSC resulted in no consistent spatial patterns, and no discernable correspondence with local-scale environmental factors. This study demonstrates the importance of local-scale environmental factors to mercury bioaccumulation in topographically heterogeneous landscapes, and provides evidence that food-chain length can be an important predictor of broad-scale differences in Hg bioaccumulation among streams.

New York, South Carolina↗

USGS2011

Histologic, immunologic and endocrine biomarkers indicate contaminant effects in fishes of the Ashtabula River

The use of fish as sentinels of aquatic ecosystem health is a biologically relevant approach to environmental monitoring and assessment. We examined the health of the Ashtabula River using histologic, immunologic, and endocrine biomarkers in brown bullhead (BB; Ameiurus nebulosus) and largemouth bass (Micropterus salmoides) and compared fish collected from a reference site (Conneaut Creek). Seasonal analysis was necessary to distinguish differences in fish between the two rivers. Overall BB from the Ashtabula River had a lower condition factor and significantly more macrophage aggregates than those from the reference site. Reduced bactericidal and cytotoxic-cell activity was observed in anterior kidney leukocytes from both BB and largemouth bass from the Ashtabula River. Lower plasma thyroxine and triiodo-L-thyronine in both species in the Ashtabula River indicated disruption of the thyroid axis. Differences in physiological biomarker responses were supported by body burden chemical concentrations when data were analyzed on a seasonal basis. The use of two fish species added a level of rigor that demonstrated biological effects were not exclusive to a single species. The results provide strong evidence that contaminants have affected fish in the Ashtabula River, a Great Lakes Area of Concern, and provide a baseline by which to evaluate remediation activities.

Ohio↗

USGS2014

Characterizing lentic freshwater fish assemblages using multiple sampling methods

Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations ( N  = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

Environmental Monitoring and Assessment↗

USGS2016

From "Duck Factory" to "Fish Factory": Climate induced changes in vertebrate communities of prairie pothole wetlands and small lakes

The Prairie Pothole Region’s myriad wetlands and small lakes contribute to its stature as the “duck factory” of North America. The fishless nature of the region’s aquatic habitats, a result of frequent drying, freezing, and high salinity, influences its importance to waterfowl. Recent precipitation increases have resulted in higher water levels and wetland/lake freshening. In 2012–13, we sampled chemical characteristics and vertebrates (fish and salamanders) of 162 Prairie Pothole wetlands and small lakes. We used non-metric multidimensional scaling, principal component analysis, and bootstrapping techniques to reveal relationships. We found fish present in a majority of sites (84 %). Fish responses to water chemistry varied by species. Fathead minnows ( Pimephales promelas ) and brook sticklebacks ( Culaea inconstans ) occurred across the broadest range of conditions. Yellow perch ( Perca flavescens ) occurred in a smaller, chemically defined, subset. Iowa darters ( Etheostoma exile ) were restricted to the narrowest range of conditions. Tiger salamanders ( Ambystoma mavortium ) rarely occurred in lakes with fish. We also compared our chemical data to similar data collected in 1966–1976 to explore factors contributing to the expansion of fish into previously fishless sites. Our work contributes to a better understanding of relationships between aquatic biota and climate-induced changes in this ecologically important area.

North Dakota↗

USGS1992

Selenium and other elements in freshwater fishes from the irrigated San Joaquin valley, California

Arsenic (As), chromium (Cr), mercury (Hg), and selenium (Se) were measured in composite whole-body samples of five fishes — bluegill ( Lepomis macrochirus ), common carp ( Cyprinus carpio ), mosquitofish ( Gambusia affinis ), largemouth bass ( Micropterus salmoides ), and Sacramento blackfish ( Orthodon microlepidotus ) — from the San Joaquin River system to determine if concentrations were elevated from exposure to agricultural subsurface (tile) drainage. Except for Cr, the concentrations of these elements in fishes from one or more sites were elevated; however, only Se approached concentrations that may adversely affect survival, growth, or reproduction in warm water fishes. Moreover, only Se among the four measured elements exhibited a geographic (spatial) pattern that coincided with known inflows of tile drainage to the San Joaquin River and its tributaries. Historical data from the Grassland Water District (Grasslands; a region exposed to concentrated tile drainage) suggested that concentrations of Se in fishes were at maximum during or shortly after 1984 and have been slightly lower since then. The recent decline of Se concentrations in fishes from the Grasslands could be temporary if additional acreages of irrigated lands in this portion of the San Joaquin Valley must be tile-drained to protect agricultural crops from rising groundwater tables

California↗

USGS2017

Fish assemblages

Methods to sample fishes in stream ecosystems and to analyze the raw data, focusing primarily on assemblage-level (all fish species combined) analyses, are presented in this chapter. We begin with guidance on sample site selection, permitting for fish collection, and information-gathering steps to be completed prior to conducting fieldwork. Basic sampling methods (visual surveying, electrofishing, and seining) are presented with specific instructions for estimating population sizes via visual, capture-recapture, and depletion surveys, in addition to new guidance on environmental DNA (eDNA) methods. Steps to process fish specimens in the field including the use of anesthesia and preservation of whole specimens or tissue samples (for genetic or stable isotope analysis) are also presented. Data analysis methods include characterization of size-structure within populations, estimation of species richness and diversity, and application of fish functional traits. We conclude with three advanced topics in assemblage-level analysis: multidimensional scaling (MDS), ecological networks, and loop analysis.

Book chapter↗

USGS2025

Climate and land use drivers of freshwater fish biodiversity in the northeastern United States

Freshwater habitats can sustain high biodiversity, but habitat degradation, species invasion, and overexploitation have imperiled freshwater species. The multiple threats to freshwater habitats and changing stream characteristics due to climate change make it challenging to identify the drivers of fish vulnerability, especially given that the importance of drivers may vary by the biodiversity endpoint. The goals of this study were to 1) describe freshwater (lotic) fish biodiversity across northeastern states in the United States, and 2) identify geographic, climate, and land use drivers of fish biodiversity, toward improving freshwater fish conservation. We predicted habitat suitability for 53 fish species using survey data and corresponding geographic, climate, and land use data. After model fitting, we grouped species using a traditional approach based on traits and a new approach using modeled streamflow and stream temperature to create clusters. We found that climate and land use vulnerable groups did not always have similar geographic patterns or relationships to the climate or land use variables, suggesting that biota vulnerable to changing conditions may be overlooked by reliance on predefined guilds to set conservation goals. Biodiversity groups that were vulnerable to climate variables were also related to land use variables that can be used to identify restoration opportunities. This approach may be useful for managers interested in holistic freshwater management under changing stream conditions.

Connecticut, Maine, Massachusetts, New Hampshire, ↗

USGS2007

Trends of brominated diphenyl ethers in fresh and archived Great Lakes fish (1979-2005)

While few environmental measurements of brominated diphenyl ethers (BDEs) were completed prior to the mid-1990s, analysis of appropriately archived samples might enable the determination of contaminant trends back to the introduction of these chemicals. In this paper, we first investigate the stability of BDEs in archived frozen and extracted fish samples, and then characterize trends of these chemicals in rainbow smelt ( Osmerus mordax ) and lake trout ( Salvelinus namaycush ) in each of the Great Lakes between 1979 and 2005. We focus on the four most common congeners (BDE-47, 100, 99 and 153) and use a change-point analysis to detect shifts in trends. Analyses of archived fish samples yielded precise BDE concentration measurements with only small losses (0.8% per year in frozen fish tissues, 2.2% per year in refrigerated extracts). Trends in fish from all Great Lakes showed large increases in BDE concentrations that started in the early to mid-1980s with fairly consistent doubling times (generally 2–4 years except in Lake Erie smelt where levels increased very slowly), though concentrations and trends show differences by congener, fish species and lake. The most recent data show that accumulation rates are slowing, and concentrations of penta- and hexa-congeners in trout from Lakes Ontario and Michigan and smelt from Lake Ontario started to decrease in the mid-1990s. Trends in smelt and trout are evolving somewhat differently, and trout concentrations in the five lakes are now ranked as Michigan > Superior = Ontario > Huron = Erie, and smelt concentrations as Michigan > Ontario > Huron > Superior > Erie. The analysis of properly archived samples permits the reconstruction of historical trends, congener distributions, biomagnification and other information that can aid the understanding and management of these contaminants.

Chemosphere↗

USGS2010

A comparison of algal, macroinvertebrate, and fish assemblage indices for assessing low-level nutrient enrichment in wadeable Ozark streams

Biotic indices for algae, macroinvertebrates, and fish assemblages can be effective for monitoring stream enrichment, but little is known regarding the value of the three assemblages for detecting perturbance as a consequence of low-level nutrient enrichment. In the summer of 2006, we collected nutrient and biotic samples from 30 wadeable Ozark streams that spanned a nutrient-concentration gradient from reference to moderately enriched conditions. Seventy-three algal metrics, 62 macroinvertebrate metrics, and 60 fish metrics were evaluated for each of the three biotic indices. After a group of candidate metrics had been identified with multivariate analysis, correlation procedures and scatter plots were used to identify the four metrics having strongest relations to a nutrient index calculated from log transformed and normalized total nitrogen and total phosphorus concentrations. The four metrics selected for each of the three biotic indices were: algae—the relative abundance of most tolerant diatoms, the combined relative abundance of three species of Cymbella , mesosaprobic algae percent taxa richness, and the relative abundance of diatoms that are obligate nitrogen heterotrophs; macroinvertebrate—the relative abundance of intolerant organisms, Baetidae relative abundance, moderately tolerant taxa richness, and insect biomass; fish—herbivore and detritivore taxa richness, pool species relative abundance, fish catch per unit effort, and black bass ( Micropterus spp.) relative abundance. All three biotic indices were negatively correlated to nutrient concentrations but the algal index had a higher correlation (rho = −0.89) than did the macroinvertebrate and fish indices (rho = −0.63 and −0.58, respectively). Biotic index scores were lowest and nutrient concentrations were highest for streams with basins having the highest poultry and cattle production. Because of the availability of litter for fertilizer and associated increases in grass and hay production, cattle feeding capacity increases with poultry production. Studies are needed that address the synergistic effect of poultry and cattle production on Ozark streams in high production areas before ecological risks can be adequately addressed.

Arkansas, Oklahoma↗