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USGS1994

Instream flows to assist the recovery of endangered fishes of the upper Colorado River basin

The riverine landscape of the upper Colorado River basin has been extensively modified by dams, diversions, revetments, and water abstractions. These changes, probably coupled with the introduction of many nonnative fishes, have compromised the existence of four of the native fishes (Colorado River squawfish Ptychocheilus lucius, humpback chub Gila cypha, bonytail chub Gila elegans, and razorback sucker Xyrauchen texanus) of the river system. Efforts to recover these endangered fishes have emphasized reregulation of flows to provide better habitat conditions than existed during the last half century, when ranges and abundances of the fishes declined significantly. Contention emerged, however, with regard to the efficacy of methods used by the U.S. Fish and Wildlife Service to justify flow recommendations to protect the endangered fishes. The purpose of this study was to review the science pertaining to the issue of flow provision, to identify critical uncertainties, and to provide recommendations for determining the instream flow needs of the endangered fishes.

Biological Report↗

USGS2020

Predictive relations between acid-base chemistry and fish assemblages in streams of the Adirondack Mountains

Surface waters across much of New York State’s Adirondack Mountains were acidified in the late 20th century but began to recover following the 1990 Title IV Amendments to the Clean Air Act. Previous assessments of acidification recovery in the Adirondacks have generally been based on surface water chemistry data and inferred relationships to fish and other aquatic biota. Little data, however, has been available to characterize biological impacts and predict recovery of fish assemblages in streams of the region. Here, we use quantitative fish surveys combined with chemistry data from 48 headwater streams sampled during summer 2014–2016 to develop logistic (probability) models that characterize the status of contemporary fish assemblages and predict how different N and S deposition loads may affect future fish assemblages. Statistical models for inorganic aluminum (Al i ) and richness ≥1 species; and for acid neutralizing capacity (ANC) and total density >400 fish/0.1 ha, total biomass >1500 g/0.1 ha, brook trout Salvelinus fontinalis density >0 or >200 fish/0.1 ha, and brook trout biomass >1000 g/0.1 ha were suitable for evaluating community and population responses to changes in acid-base chemistry. Predictions of fish-assemblage responses using several of these models demonstrated that anticipated changes in national (U.S.) secondary standards for atmospheric emissions of NO x and SO x to achieve target N and S deposition loads are likely to alter the acid-base chemistry and the probabilities of observing various levels of brook trout population and fish-community metrics in streams across the region and elsewhere.

New York↗

USGS2021

Status and trends of pelagic and benthic prey fish populations in Lake Michigan, 2020

Lakewide acoustic (AC) and bottom trawl (BT) surveys are conducted annually to generate indices of pelagic and benthic prey fish densities in Lake Michigan. The BT survey had been conducted each fall from 1973 through 2019 using 12-m trawls at depths ranging from 9 to 110 m and included 70 fixed locations distributed across seven transects; this survey estimates densities of seven prey fish species (i.e., alewife, bloater, rainbow smelt, deepwater sculpin, slimy sculpin, round goby, ninespine stickleback) as well as for age-0 yellow perch and large burbot. The AC survey, which serves to estimate densities of three prey fish species (i.e., alewife, bloater, and rainbow smelt), had been conducted each late summer/early fall from 2004-2019. The data generated from these surveys are used to estimate various population parameters that are, in turn, used by state and tribal agencies in managing Lake Michigan fish stocks. The 2020 COVID-19 pandemic severely limited the Lake Michigan pelagic and benthic prey fish surveys. While the AC survey was not conducted, 32 tows across three of seven standard BT transects (Saugatuck, Waukegan and Port Washington) were completed during an abbreviated survey. Total prey fish biomass density from the abbreviated BT survey was 1.91 kg/ha, continuing a recent trend of historically low estimates below the long-term (i.e., 1973-2020) average of 34.94 kg/ha. Mean biomass of yearling and older (YAO) alewives in 2020 was 0.025 ± 0.017 kg/ha, tied for the lowest ever recorded on the BT survey. No age-0 alewife were captured in the bottom trawl and of the limited number (n=16) of alewife collected, none were older than age four. Bloater (1.39 kg/ha) and deepwater sculpin (0.47 kg/ha) accounted for greatest proportion of biomass in the BT survey, while biomass density of slimy sculpin, round goby and rainbow smelt were all ≤ 0.01 kg/ha. While caution must be taken when interpreting the results of the abbreviated BT survey, the estimates suggest that prey fish densities remain well below historical values.

Lake Michigan↗

USGS2021

Monitoring the recovery of seabirds and forage fish following a major ecosystem disruption in Lower Cook Inlet

Following the North Pacific marine heatwave of 2014-2016 and associated extreme die-off of seabirds in the winter of 2015-2016, we repeated historical marine bird and forage fish surveys around two seabird colonies (Gull Island, Chisik Island) in lower Cook Inlet during 2016-2019 in order to document immediate and lingering impacts of the heatwave on resident fish and seabird populations. At sea, we conducted acoustic/trawl surveys for fish in near-colony areas, while simultaneously counting seabirds on survey transects. At colonies, we monitored bird numbers on whole colony censuses and population plot counts and assessed annual reproductive success of Black-legged Kittiwakes ( Rissa tridactyla ) and Common Murres ( Uria aalge ). Our studies suggest that impacts of the heatwave on seabirds and their forage base were severe and extended for several years beyond the heatwave itself. Although fish biomass indices were greatest in 2016-2017, the forage community was largely dominated by juvenile fish with low nutritional value following a collapse of key species of forage fish during the marine heatwave. Lowest fish biomass was observed in 2018, coincident with a marked decline in the at-sea abundance of many seabirds around colonies. By 2019 there were signs of improvement in prey abundance and quality, and significant aggregations of pre-spawning capelin and large sand lance were observed in and around Kachemak Bay. In comparison with historical (1996-1999) bird colony surveys, kittiwake population counts decreased by more than 70% at Chisik Island, and by 8-29% at Gull Island. Similarly, murre counts decreased at Chisik Island by 72% and by more than 20% at Gull Island. Kittiwakes had complete reproductive failure at Chisik Island from 2016-2018, with minimal success in 2019. At Gull Island, kittiwakes also failed in 2016 and 2018 but had unusually high productivity in 2017 and 2019. Murres also had complete reproductive failures at Chisik Island in all four years and at Gull Island during 2016, 2017 and 2018. Murres finally fledged chicks in 2019, albeit at about half the normal rate. Finally, we also observed unusually high levels of predator disturbance (egg predation, flushing adults from plots) and unprecedented numbers of adult birds in poor body condition (“skinny murres”), particularly in 2018. Together, these results indicate that an extreme disruption of marine food webs occurred during and after the heatwave. Given the prolonged reproductive failures, continued monitoring is required to assess continuing impacts and recovery from the 2014-2016 heatwave. For example, murre chicks that would have been produced in 2016 should, after 4-5 years away, start recruiting to the colony in 2021, and thereby replace aged adults that would have died naturally in the past year(s). Without such natal recruitment for at least the next 3-4 years, we should document a continuing decline in bird numbers at the colonies.

Alaska↗

USGS2022

Lake Ontario April prey fish survey results and Alewife assessment, 2022

The annual Lake Ontario April bottom trawl survey and Alewife, Alosa pseudoharengus , population assessment provide science to inform management decisions related to predator-prey balance and fish community dynamics. The 2022 survey was conducted from March 31 to April 26, included 235 trawls in the main lake and embayments, and sampled depths from 5 to 219 m (16 – 723 ft). The survey captured 311,770 fish from 30 species with a total weight of 7,740 kg (17,028 lbs.). Alewife were 85% of the catch by number while Rainbow Smelt, Osmerus mordax , Round Goby, Neogobius melanostomus , and Deepwater Sculpin, Myoxocephalus thompsonii , comprised 6%, 4%, and 4% of the catch, respectively. The 2022 biomass index for Rainbow Smelt decreased 80% relative to the high values observed in 2021 as did the value for Cisco, Coregonus artedi , (46% decline). Emerald Shiner, Notropis atherinoides , biomass index increased in 2021 and Threespine Stickleback, Gasterosteus aculeatus , biomass remained low. No Bloater, Coregonus hoyi , were captured during the 2022 survey. In 2022, Alewife biomass in U.S. waters (58.1 kilograms per hectare, kg·ha-1) was substantially higher than Canadian waters (26.3 kg·ha-1). The 2022 Alewife biomass index (41.6 kg·ha-1) decreased 10% from 2021 while the 2022 density index decreased 62% from 2021. Prediction modeling indicated the growth of the abundant 2020 Alewife year class, sampled as age-1 fish in 2021, would cause the adult Alewife biomass to increase in 2022. Although the adult Alewife biomass did increase relative to 2021 (61%), the increase was lower than predicted. The difference between the predictions and observations was because survival of age-1 fish from 2021 to 2022 was lower than had previously been observed. In the three previous years of observations the proportion of age-1 Alewife surviving to age 2 ranged from 0.33 to 0.53; however, that proportion was only 0.21 from 2021 to 2022. Survival estimates of Alewife age-5 through age-8 were higher than previously observed, possibly because salmonid predation focused on the abundant younger Alewife. The catch of age-1 Alewife in 2022, which is a measure of reproductive success in 2021, was below average and similar to the abundances of the 2018 and 2019 year classes. Simulation modeling results indicated the adult Alewife biomass is likely to increase slightly in 2023, whereas predictions for 2024 are less certain. Hydroacoustic sampling was used to estimate prey fish densities in open-water, pelagic habitats not sampled by the bottom trawl. Bottom trawl-based densities from the lake bottom were at least 25 times greater than densities of prey fish in the water column above the trawl. These results support the idea that, in April, when the warmest, most dense water is on the lake bottom, Alewife and most other pelagic prey fish primarily inhabit deep, near bottom habitats and can be effectively sampled with bottom trawling.

Lake Ontario↗

USGS2022

Framework for the development of the Columbia River mainstem fish tissue and water quality monitoring program - Bonneville Dam to Canadian border

The Columbia River provides important cultural, economic, and ecological services to a significant portion of the United States. Anadromous and resident fish species and other wildlife are integrated into the cultural traditions of all Tribes in the Columbia River Basin. Salmon, lamprey, sturgeon, and resident fish are an integral part of Tribal religion, culture, and physical sustenance. Despite concerns about the effect of contaminants on the aquatic ecosystem, the disproportionate effects of contaminants on members of Tribal sovereignties, and the known effects of contaminants on species protected under the Endangered Species Act, efforts to address toxic chemical pollution in the Columbia River have been limited. The lack of a dedicated contaminant monitoring program impedes evaluation and decision making regarding the health of the Columbia River ecosystem, as well as human health for Tribal members and others that consume fish and other biota from the Columbia River. The purpose of this framework is to provide guidance for the development of a long-term program (Program) that provides the basis for assessing the status and trends of contaminants in fish, sediment, water, and invertebrates along the 962-kilometer length of the Columbia River from the Bonneville Dam upriver to the Canadian Border (Figure ES1). This framework will focus on four persistent and bioaccumulative classes of toxic contaminants: • Mercury • Polychlorinated biphenyls (PCBs) • Dichlorodiphenyltrichloroethane (DDT) • Polybrominated diphenyl ethers (PBDEs) Media of interest in this framework include anadromous and resident fish, sediment, invertebrates, biofilm, and surface water. Future consideration of additional contaminants could include pesticides, per or poly-fluoroalkyl substances, 6PPD-quinone, and contaminants of emerging concern (CECs), which comprises a diverse group of anthropogenic chemicals that include thousands of pharmaceuticals, hormones, illicit drugs, new pesticides, personal care products, flame retardants, artificial sweeteners, perfluorinated compounds, disinfection byproducts, ultraviolet filters, and other industrial chemicals. This framework includes the vision, goals, and objectives for the Program. The vision for the Program is that it will provide the basis for assessing the status and trends of contaminants in the Columbia River to guide ecosystem recovery resulting in clean, healthy fish for current and future generations . The goals of the Program are to 1) conduct long-term monitoring to assess the spatial and temporal status and trends of toxics in fish, water, sediment, and other potential media in the Columbia River mainstem, from Bonneville Dam to the Canadian Border in perpetuity, 2) stimulate conversion of science into action by providing information to facilitate future decision making that improves ecosystem function and reduces contaminants in all levels of the food chain, and 3) adaptively manage the Program to address new key questions, incorporate new and emerging science advancements, and respond to community information needs. To facilitate achieving these goals, this framework provides details on technical planning; community outreach and engagement; and adaptive management to promote understanding and improve future decision making over the long-term, including updating the Program with new and emerging science and community needs. Additionally, data associated with the Program will be made available to the public through the EPA Water Quality Exchange (https://www.epa.gov/waterdata/water-quality-data). Documents and other materials associated with the Program can be accessed via a website hosted by Yakama Nation Fisheries (https://yakamafish-nsn.gov/restore/projects/columbia-river-mainstem- water-quality-monitoring-program). Although the Program is limited to the Columbia River upstream of the Bonneville Dam, collaboration with other entities that monitor contaminants in the Columbia River Basin, including the Columbia River estuary below Bonneville Dam, are also an important component of outreach. Our goal is to encourage efforts to ensure data comparability across programs and recognize that the growth and adaptive management of the Program considers basin-wide monitoring developments.

Oregon, Washington↗

USGS2024

Status and trends of the Lake Huron prey fish community, 1976-2023

The U. S. Geological Survey-Great Lakes Science Center has monitored annual changes in the offshore (depth >9m) prey fish community of Lake Huron since 1973. Monitoring of prey fish populations in Lake Huron is based on a bottom trawl survey that targets demersal (benthic) species and an acoustic-midwater trawl survey that targets pelagic species and life stages. In 2023, Bloater ( Coregonus hoyi ) accounted for 77% of the main basin biomass in bottom trawls and 86% of the main basin biomass in the acoustics survey. Despite this sustained importance of native species in the main basin, species diversity is below desired levels. Bloater in the main basin has exhibited population growth and strong recruitment in recent years, and Cisco ( Coregonus artedi ) has exhibited increased biomass in the North Channel since 2015. In contrast non-native Alewife ( Alosa pseudoharengus ), whose population collapsed in 2004 and has not recovered, were less than 1% of fish biomass in 2023. Rainbow Smelt ( Osmerus mordax ) accounted for 7% of the main basin biomass in bottom trawls and 22% of the main basin biomass in the acoustics survey. Despite remaining the second-most abundant prey species in the main basin, Rainbow Smelt has not shown appreciable increases in biomass despite recent strong year classes. Deepwater Sculpin ( Myoxocephalus thompsonii ) increased by 47% in 2023 and were 33% of the long-term average. Slimy Sculpin ( Cottus cognatus ) increased to 60% of the long-term average but remained rare in bottom trawl catches. In contrast, biomass of Round Goby ( Neogobius melanostomus ), a non-native species similar ecologically to the sculpin species, remained near the record high biomass reached in 2022. Current lake conditions characterized by ongoing oligotrophication seem to favor native coregonines over non-native fishes. Use of complementary surveys (bottom trawl, acoustics) remains important for evaluating prey fish status in Lake Huron, where prey fish community dynamics vary by basin and prey fish responses to changing environmental conditions depend on species and/or habitat.

Lake Huron↗

USGS2023

Effects of sucker gigging on fish populations in Oklahoma scenic rivers

Suckers (Catostomidae) are ecologically important, and some support popular fisheries, despite not being considered ‘sport fish’ in most states. Gigging suckers is a popular and culturally significant pastime in the Ozark Highlands, but little is known about the effect of gigging harvest on population dynamics of suckers. Therefore, research is needed to determine safe levels of sucker harvest that ensure sustainability of sucker gigging and protect overall ecosystem function. The objectives of this study were to: 1) determine the spatial distribution of common sucker species during spawning season (when sucker gigging is most effective), 2) determine the population size, age structure , and total mortality rate for common sucker species, and 3) model the effects of different harvest rates on sucker populations to determine the harvest rate at which growth overfishing and recruitment overfishing begin. Suckers were sampled using electrofishing, modified fyke netting, gillnetting, hoop netting, and seining and marked with passive integrated transponder (PIT) tags to provide information about population size, demographics, and coarse-scale movement patterns. A subset of fish sampled using the above gears and additional fish collected during gigging tournaments in 2017-2019 and 2021-2022 (no tournament was held in 2020) were used for age analyses. Tournament data collected prior to the initiation of this project were obtained from the state agency. Data from gigging tournaments indicated Golden Redhorse Moxostoma erythrurum, Black Redhorse M. duquesnei, White Sucker Catostomus commersonii, and Spotted Sucker Minytrema melanops were vulnerable to gigging harvest. Selection by giggers for larger individuals was apparent for all species except Golden Redhorse in 2019. Spotted Suckers constituted most fish harvested, but the proportion of each species harvested still varied among years. A total of 943 fish were aged from samples obtained from 2017 to 2022 and results from subsequent analyses indicated a high degree of variation in growth rates within and among species. Over 4,700 suckers were tagged with PIT tags and over 400 recaptures of these tagged fish were made since autumn 2018. Preliminary analyses indicate survival was consistent across samples and species, and detection rates varied by sampling event (3-month periods). Our most likely top multistrata model suggested that a large portion of fish within the upper Spavinaw, lower Spavinaw, and reservoir sections remain in these locations year-round (means: 0.46 – 0.67). Despite this, transition probabilities are still high for movement from upper Spavinaw to lower Spavinaw (mean: 0.32) and from lower Spavinaw to upper Spavinaw (mean: 0.38). Likewise, transition probabilities were high for movement from lower Spavinaw to the reservoir (mean: 0.15) and from the reservoir to lower Spavinaw (mean: 0.32). Transition probabilities between upper Spavinaw and the reservoir were low in both directions (means < 0.01). Population sizes, growth trajectories and length-weight relationships varied among species. Preliminary harvest models suggest species-specific regulation may be scientifically appropriate; however, it may be difficult for giggers to identify species while gigging. Based on our model results, there appears to be little risk of recruitment or growth overfishing for any species at current exploitation levels.

Oklahoma↗

USGS1995

Southeastern freshwater fishes

North America has the richest fauna of temperate freshwater fishes in the world, with about 800 native species in the waters of Canada and the United States. The center of this diversity is in the southeastern United States, where as many as 500 species may exist (62% of the continental fauna north of Mexico). Many coastal marine species also enter fresh waters of the Southeast, and at least 34 foreign fish species are established in the region. Although freshwater fishes of the United States are better studied than any fish fauna of comparable scope in the world (Lee et al. 1980; Hocutt and Wiley 1986; Matthews and Heins 1987; Page and Burr 1991; Mayden 1992), large gaps exist in scientific knowledge about the biology and ecology of most species. New species are still being discovered, and the taxonomy of other species is being refined. Seriously declining populations of freshwater fishes in the United States concern the scientific community (Deacon et al. 1979; Williams et al. 1989; Moyle and Leidy 1992; Warren and Burr 1994). This article briefly summarizes the current conservation status of southeastern freshwater fishes; the Southeast is emphasized because of its important fish biodiversity and to focus attention on the growing problem of adverse human impacts on the region's aquatic habitats (Mount 1986; Burkhead and Jenkins 1991; Etnier and Starnes 1991; Warren and Burr 1994).

Book chapter↗

USGS2001

A national pilot study of mercury contamination of aquatic ecosystems along multiple gradients" Bioaccumulation in fish

Water, sediment, and fish were sampled in the summer and fall of 1998 at 106 sites from 20 U.S. watershed basins to examine relations of mercury (Hg) and methylmercury (MeHg) in aquatic ecosystems. Bioaccumulation of Hg in fish from these basins was evaluated in relation to species, Hg and MeHg in surficial sediment and water, and watershed characteristics. Bioaccumulation was strongly (positively) correlated with MeHg in water (r = 0.63, p < 0.001) but only moderately with the MeHg in sediment (r = 0.33, p < 0.001) or total Hg in water (r = 0.28, p < 0.01). Of the other significantly measured parameters, pH, DOC, sulfate, sediment LOI, and the percent wetlands of each basin were also significantly correlated with Hg bioaccumulation in fish. The best model for predicting Hg bioaccumulation included Me Hg in water, PH of the water, % wetlands in the basin, and the AVS content of the sediment. These four variables accounted for 45% of the variability of the fish fillet Hg concentration normalized (divided) by total length; however, the majority was described by MeHg in water. A MeHg water concentration 0.12 ng/L was on average, associated with a fish fillet Hg concentration of 0.3 mg/kg wet weight for an age-3 fish when all species were considered. For age-3 largemouth bass, a MeHg water concentration of 0.058 ng/L was associated with the 0.3 mg/kg fillet concentration. Based on rankings for Hg in sediment, water, and fish, sampling sites from the following five study basins had the greatest Hg contamination: Nevada Basin and Range, South Florida Basin, Sacramento River Basin (California), Santee River Basin and Caostal Drainages (South Carolina), and the Long Island and New Jersey Coastal Drainags. A sampling and analysis strategy based on this pilot study is planned for all USGS/NAWQA study units over the next decade.

Biological Science Report↗

USGS1999

Biomonitoring of Environmental Status and Trends (BEST) Program: Field Procedures for Assessing the Exposure of Fish to Environmental Contaminants

This document describes procedures used to collect information, tissues, and fluids for documenting the exposure of fish to environmental contaminants. For the procedures described here, fish are captured (preferably by electrofishing) and held alive until processing (generally <1 h). Fish are weighed, measured, and examined for grossly visible external lesions and pathologies. A blood sample is collected by caudal veinipuncture using a needle and syringe. The fish is subdued and it's abdominal cavity opened. The internal organs are dissected from the fish for examination. The sex of the fish is determined by direct observation of its gonads. The liver is weighed (most species) and cut into small cubes and flash-frozen in cryogenic vials, which are stored and shipped in dry ice or liquid nitrogen. Additional liver cubes plus all grossly visible anomalies are preserved for histopathology. The gonads and spleen are weighed, and samples are preserved for histopathology. The kidneys are examined, and histopathology samples collected. A gill sample is also collected and preserved. All remaining tissues are returned to the carcass, which is wrapped in foil, labeled for chemical analysis, and chilled. Individual fish carcasses are composited by station, species, and gender; frozen; and shipped to the analytical laboratory. Procedures are also described for record keeping; processing blood to obtain serum and plasma; flash-freezing samples; cleaning equipment; and preventing the transport of living organisms among waterways. A list of necessary equipment and supplies is also provided.

Information and Technology Report↗

USGS2006

Relationships between reef fish communities and remotely sensed rugosity measurements in Biscayne National Park, Florida, USA

The realization that coral reef ecosystem management must occur across multiple spatial scales and habitat types has led scientists and resource managers to seek variables that are easily measured over large areas and correlate well with reef resources. Here we investigate the utility of new technology in airborne laser surveying (NASA Experimental Advanced Airborne Research Lidar (EAARL)) in assessing topographical complexity (rugosity) to predict reef fish community structure on shallow (<10 m deep) patch reefs. Marine portions of Biscayne National Park, Florida, USA, were surveyed remotely using the EAARL, and reef fish populations were visually surveyed on 10 patch reefs at independent, randomly selected stations ( n = 10–13 per reef). Rugosity at each station was assessed in situ by divers using the traditional chain-transect method (10-m scale), and remotely using the EAARL submarine topography data at multiple spatial scales (2, 5, and 10 m). The rugosity and biological datasets were analyzed together to elucidate the predictive power of EAARL rugosity in describing the variance in reef fish community variables and to assess the correlation between chain-transect and EAARL rugosity. EAARL rugosity was not well correlated with chain-transect rugosity, or with species richness of fishes (although statistically significant, the amount of variance explained by the model was very low). Variance in reef fish community attributes was better explained in reef-by-reef variability than by physical variables. However, once the reef-by-reef variability was taken into account in a two-way analysis of variance, the importance of rugosity could be seen on individual reefs. Fish species richness and abundance were statistically higher at high rugosity stations compared to medium and low rugosity stations, as predicted by prior ecological research. The EAARL shows promise as an important mapping tool for reef resource managers as they strive to inventory and protect coral reef resources.

Florida↗

USGS2001

Fish species and community distributions as proxies for sea-floor habitat distributions: the Stellwagen Bank National Marine Sanctuary example (northwest Atlantic, Gulf Of Maine)

Defining the habitats of fishes and associated fauna on outer continental shelves is problematic given the paucity of data on the actual types and distributions of seafloor habitats. However many regions have good data on the distributions of fishes from resource surveys or catch statistics because of the economic importance of the fisheries. Fish distribution data (species or communities) have been used as a proxy for the distribution of habitats to develop precautionary conservation strategies for habitat protection (e.g., marine protected areas, fishing gear restrictions). In this study we assessed the relationships between the distributions of fish communities and species derived from trawl survey data with the spatial distribution of sediment types determined by sampling and acoustic reflectance derived from multibeam sonar surveys in Stellwagen Bank National Marine Sanctuary. Fish communities were correlated with reflectance values but all communities did not occur in unique sediment types. This suggests that use of community distributions as proxies for habitats should include the caveat that a greater number of communities within an area could indicate a greater range of habitat types. Single species distributions showed relationships between abundance and reflectance values. Trawl catches with low abundances had wide variations in reflectance values while those with high abundances had narrower ranges indicating habitat affinities. Significant non-random frequency-dependent relationships were observed for 17 of 20 species although only 12 of 20 species had significant relationships based on rank correlation. These results suggest that species distributions based on trawl survey data can be used as proxies for the distribution of seafloor habitats. Species with known habitat associations can be used to infer habitat requirements of co-occurring species and can be used to identify a range of habitat types.

Massachusetts↗

USGS2009

Ecology of stream fish: Insights gained from an individual-based approach to juvenile Atlantic salmon

Using data from an ongoing study of juvenile Atlantic salmon growth and survival in tributaries of the Connecticut River, USA, we compare standard population-level approaches to those focusing on individuals. We highlight the potential benefits of resampling individually tagged stream fish as compared to standard approaches. Specifically we focus on growth, survival, movements and population estimation. The advantages of estimating sizes and growth rates from individual size trajectories include obtaining growth histories and the ability to perform retrospective analysis of the consequences of different life-history strategies. An example might be the patterns of growth leading to either early maturity or migration. Resampling known individuals is the only way we know to chart both short-term and long-term movements and to assign growth and mortality consequences to such movements. Finally, individual-level data permit robust estimation of survival and density/abundance using methods such as Cormack/Jolly-Seber. The results indicate that population estimates were about 10% lower using individual data than using population data, that survival from sample to sample was typically >90%, that the majority of recaptured fish did not move during the summer, that growth was rapid during spring and most fish lost mass during the summer and that growth trajectories for maturing and non-maturing fish showed substantially different patterns. An individual-based approach to stream fish ecology provides the opportunity to explore the mechanisms responsible for population-level patterns but comes at the cost of significant field effort. Tradeoffs between increased data resolution and the effort required to obtain the data must be considered before undertaking individual-based field studies of stream fishes.

Massachusetts↗

USGS2013

Links between riparian landcover, instream environment and fish assemblages in headwater streams of south-eastern Brazil

We hypothesised and tested a hierarchical organisation model where riparian landcover would influence bank composition and light availability, which in turn would influence instream environments and control fish assemblages. The study was conducted during the dry season in 11 headwater tributaries of the Sorocaba River in the upper Paraná River Basin, south-eastern Brazil. We focused on seven environmental factors each represented by one or multiple environmental variables and seven fish functional traits each represented by two or more classes. Multivariate direct gradient analyses suggested that riparian zone landcover can be considered a higher level causal factor in a network of relations that control instream characteristics and fish assemblages. Our results provide a framework for a hierarchical conceptual model that identifies singular and collective influences of variables from different scales on each other and ultimately on different aspects related to stream fish functional composition. This conceptual model is focused on the relationships between riparian landcover and instream variables as causal factors on the organisation of stream fish assemblages. Our results can also be viewed as a model for headwater stream management in that landcover can be manipulated to influence factors such as bank composition, substrates and water quality, whereas fish assemblage composition can be used as indicators to monitor the success of such efforts.

Sorocaba River Basin↗

USGS2018

Multiple metrics provide context for the distribution of a highly mobile fish predator, the blue catfish

Data sets with increased spatial and temporal resolution can help researchers and resource managers quantify representative distributional patterns of mobile sportfish. In this research, first, we illustrate patterns of sportfish distribution using individual ( percent of population, residence time, number of movements ) and combined distributional metrics. Second, we apply these metrics to one highly mobile fish species, the blue catfish ( Ictalurus furcatus ), across a range of spatial (whole reservoir, region, site) and temporal (year, month, diel period) scales. Specifically, we tracked 123 acoustically tagged blue catfish with a 20-receiver array in Milford Reservoir, KS, USA. When we integrated metrics, four site-specific distributional patterns emerged: (a) a large, active multi-site fish aggregation, (b) localised site fidelity, (c) transitional sites and (d) rarely used locations. These patterns would not have been detected using a single metric as each measurement revealed a different piece of the distribution story. For example, if we had only quantified percent of population, we could identify fish location, but not whether individual fish spent time at a location or were just passing through. Our examination of multiple scales also provided a novel context for interpreting site-specific patterns. As an illustration of this insight, using conventional approaches, we would have observed heterogeneity, but we would not have detected fish aggregations, in which individual fish either remained or repeatedly returned to a site. In summary, our results show the advantage of setting the entire ecosystem as the study boundary to integrate multiple responses using a spatially and temporally extensive data set.

Kansas↗

USGS2019

Historical changes in fish communities in urban streams of the southeastern U.S. and the relative importance of water-quality stressors

A total of 71 stream sites representing a gradient of urban land use was sampled across the Piedmont of the southeastern U.S. in 2014. Fish data collected (observed) at each site were compared to an expected community based on georeferenced historical (~1950 - ~1990) species occurrence records for stream segments (1:100,000 scale) containing the sampled stream sites. Loss of expected fish species (percent of fish species expected to occur but not observed) and homogenization (difference in Jaccard’s similarity of the fish community among sites observed and expected) were determined. On average, there was a 13.2% increase in the similarity of fish communities across sites, demonstrating evidence of community homogenization. Occurrence of Redbreast Sunfish (Lepomis auritus), Green Sunfish (L. cyanellus), and Bluegill (L. macrochirus) increased more than 50% over time (between observed and expected). Species loss increased significantly with urbanization whereas homogenization was not related to urbanization. Random forest analysis indicated that herbicides, insecticides, and centrarchid species richness were significant predictors of species loss. Of these, generalized additive model regression indicated that herbicides represented the most parsimonious model based on a single predictor. Stream base flow, elevation, and total nitrogen were significant predictors of homogenization. Generalized additive model regression indicated that decreased stream base flow was the single most important factor associated with increased homogenization. Chemical contaminants and associated ecosystem alteration and changes in stream flow may represent important regional influences on changes in fish communities in urban streams in the southeastern U.S.

Alabama, Georgia, North Carolina, South Carolina, ↗

USGS2007

Use of seasonal freshwater wetlands by fishes in a temperate river floodplain

This study examined the use of freshwater wetland restoration and enhancement projects (i.e. non-estuarine wetlands subject to seasonal drying) by fish populations. To quantify fish use of freshwater emergent wetlands and assess the effect of wetland enhancement (i.e. addition of water control structures), two enhanced and two unenhanced emergent wetlands were compared, as well as two oxbow habitats within the Chehalis River floodplain. Eighteen fish species were captured using fyke nets and emigrant traps from January to the beginning of June, with the most abundant being three-spined stickleback Gasterosteus aculeatus and Olympic mudminnow Novumbra hubbsi . Coho salmon Oncorhynchus kisutch was the dominant salmonid at all sites. Enhanced wetlands, with their extended hydroperiods, had significantly higher abundances of yearling coho salmon than unenhanced wetlands. Both enhanced and unenhanced emergent wetlands yielded higher abundances of non-game native fishes than oxbow habitats. Oxbow habitats, however, were dominated by coho salmon. Fish survival in the wetland habitats was dependent on emigration to the river before dissolved oxygen concentrations decreased and wetlands became isolated and stranding occurred. This study suggests that wetland enhancement projects with an outlet to the river channel appear to provide fishes with important temporary habitats if they have the opportunity to leave the wetland as dissolved oxygen levels deteriorate.

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