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USGS2023

Invasive Brook Stickleback Culaea inconstans occurrence, habitat drivers, and spatial overlap with native fishes in Wyoming, USA

A central focus of modern fisheries management is eradicating invaders that threaten imperiled native fishes. However, vast landscapes and limited funding and personnel resources demand a prioritized approach to management. Brook Stickleback Culaea inconstans (Kirtland, 1840) is an aquatic invasive species in Wyoming, USA, that may pose a risk to native biodiversity. Our aim was to evaluate Brook Stickleback’s invasive potential in the North Platte River drainage. We updated the current distribution of Brook Stickleback, evaluated for possible range expansion, and determined landscape-level habitat drivers and occurrence potential for streams across the North Platte River drainage. Additionally, we examined Brook Stickleback’s spatial overlap with native nongame fishes. At the landscape scale, Brook Stickleback preferred low-gradient streams with moderate disturbance risk. Though we did not find evidence of current Brook Stickleback range expansion 61% of streams in the drainage have landscape-level environmental characteristics that are likely suitable for Brook Stickleback, creating potential for future expansion. Brook Stickleback overlapped spatially with 13 native nongame species, though spatial overlap was less common than expected for species with similar habitat preferences. Our work serves as a case study of the factors to consider when assessing a species’ invasive potential in a previously unstudied region.

Wyoming↗

USGS2024

Supporting climate adaptation for rural Mekong River Basin communities in Thailand

Climate change impacts on large river basins, such as the Mekong River Basin (MRB), are complex due to shared governance and interconnected socioeconomic areas, making them highly vulnerable to change. The MRB, spanning six countries including Thailand, is crucial for the food and economic security of > 60 million people. However, in 2021, Thailand was ranked as the 9th highest risk country affected by climate change. To integrate climate adaptation in Thailand's MRB, we examined the effects of climate change on rapidly developing farmer and fisher communities in northeastern Thailand and explored feasible adaptation options. Using an interdisciplinary approach that included literature review, participatory action methods, and the resist-accept-direct (RAD) framework, we found that climate change is projected to increase temperatures, precipitation, extreme events, erosion, and water clarity, while decreasing heavy sediment transport. These changes negatively impact agriculture, fisheries, human health, and tourism. We identified several adaptation strategies across environmental, ecological, and human health categories to accommodate local needs, such as preventing habitat degradation (e.g., from dams and deforestation), providing fish refuge and passage, and supporting technical capacity. Community-driven adaptation planning and implementation are essential for supporting global sustainable development in a changing climate.

Mitigation and Adaptation Strategies for Global Ch↗

USGS2011

CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes

We introduce Cost Distance FISHeries (CDFISH), a simulator of population genetics and connectivity in complex riverscapes for a wide range of environmental scenarios of aquatic organisms. The spatially-explicit program implements individual-based genetic modeling with Mendelian inheritance and k -allele mutation on a riverscape with resistance to movement. The program simulates individuals in subpopulations through time employing user-defined functions of individual migration, reproduction, mortality, and dispersal through straying on a continuous resistance surface.

Conservation Genetics Resources↗

USGS2015

Development of twelve microsatellite loci in the red tree corals Primnoa resedaeformis and Primnoa pacifica

A suite of tetra-, penta-, and hexa-nucleotide microsatellite loci were developed from Roche 454 pyrosequencing data for the cold-water octocorals Primnoa resedaeformis and P . pacifica . Twelve of 98 primer sets tested consistently amplified in 30 P . resedaeformis samples from Baltimore Canyon (western North Atlantic Ocean) and in 24 P . pacifica samples (Shutter Ridge, eastern Gulf of Alaska). The loci displayed moderate levels of allelic diversity (average 7.5 alleles/locus) and heterozygosity (average 47 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and to distinguish species. These common species are long-lived (hundreds of years) and provide essential fish habitat ( P . pacifica ), yet populations are provided little protection from human activities. These loci will be used to determine regional patterns of population connectivity to inform effective marine spatial planning and ecosystem-based fisheries management.

Conservation Genetics Resources↗

USGS2015

Nine microsatellite loci developed from the octocoral, Paragorgia arborea

Paragorgia arborea, or bubblegum coral, occurs in continental slope habitats worldwide, which are increasingly threatened by human activities such as energy development and fisheries practices. From 101 putative loci screened, nine microsatellite markers were developed from samples taken from Baltimore canyon in the western North Atlantic Ocean. The number of alleles ranged from two to thirteen per locus and each displayed equilibrium. These nuclear resources will help further research on population connectivity in threatened coral species where mitochondrial markers are known to lack fine-scale genetic diversity.

Baltimore Canyon↗

USGS2017

Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population

Preservation of heritable ecological diversity within species and populations is a key challenge for managing natural resources and wild populations. Salmonid fish are iconic and socio-economically important species for commercial, aquaculture, and recreational fisheries across the globe. Many salmonids are known to exhibit ecological divergence within species, including distinct feeding ecotypes within the same lakes. Here we used 5559 SNPs, derived from RAD sequencing, to perform population genetic comparisons between two dietary ecotypes of sockeye salmon ( Oncorhynchus nerka ) in Jo-Jo Lake, Alaska (USA). We tested the standing hypothesis that these two ecotypes are currently diverging as a result of adaptation to distinct dietary niches; results support earlier conclusions of a single panmictic population. The RAD sequence data revealed 40 new SNPs not previously detected in the species, and our sequence data can be used in future studies of ecotypic diversity in salmonid species.

Alaska↗

USGS2020

A conservation-oriented SNP panel for Smallmouth Bass (Micropterus dolomieu), with emphasis on Interior Highlands lineages

The Smallmouth Bass ( Micropterus dolomieu ; SMB) is a widely distributed black bass species, but the southwestern edge of the species range within the Interior Highlands contains some of the most divergent ecotypes. The Neosho subspecies ( M. d. velox ) inhabits tributaries of the Arkansas River within the Ozark Mountains and a second lineage is reported from drainages of the Ouachita Mountains. We sought to develop a single nucleotide polymorphism (SNP) panel to (1) diagnose hybridization with sympatric Spotted Bass ( Micropterus punctulatus ; SPB) and non-native Northern SMB ( M. d. dolomieu ) stocked in the region, and (2) delineate population structure within the ranges of the Neosho and Ouachita SMB lineages. We obtained 76 individual SMB samples from across their range but concentrated within the Interior Highlands ( n = 50). We also included 3 SPB to allow for hybrid detection and 3 Shoal Bass ( Micropterus cataractae ) as an outgroup. Phylogenetic trees constructed with the generated SNP data corroborated the existence of at least three major lineages of SMB (Northern, Neosho, and Ouachita), each containing varying degrees of differentiation among major drainages. Simulation analyses revealed that chosen SNPs had high power (> 0.9) to assign SMB × SPB hybrid categories and similarly high power (> 0.8) for Northern SMB × Interior Highlands SMB hybrids. Clustering methods delineated major inter-basin population structure within the native ranges of Neosho and Ouachita SMB with chosen SNPs. Anticipated uses of the resulting 192-loci SNP panel include conservation planning, fisheries management assessments, and ecological investigations of the Neosho and Ouachita SMB lineages.

Arkansas, Missouri, Oklahoma↗

USGS2023

An amplicon genotyping panel suitable for species identification and population genetics in sauger (Sander canadensis) and walleye (Sander vitreus)

Sauger ( Sander canadensis ) and walleye ( Sander vitreus ) are closely related North American fish species that are often managed by fishery agencies throughout their ranges. However, genotyping resources for sauger are presently limited to a small set of microsatellite loci. We evaluated whether primers in an existing walleye genotyping-in-thousands panel could amplify single nucleotide polymorphism loci (SNPs) in sauger. We identified 71 primer pairs that amplify 118 SNPs in both species. Allele frequency differences were large enough to confidently distinguish the species and identify hybrids. Additionally, we identified 41 loci with observed heterozygosity > 0.1 in sauger; these markers may be useful for simple population genetic analyses and parentage analysis when few contributors are present and for differentiating highly structured populations.

Minnesota, Wisconsin↗

USGS2010

Spring distribution in Winona County, Minnesota, USA and the relationship with geologic strata in a karst landscape

Karst aquifers are important groundwater resources, but are vulnerable to contamination due to relatively rapid subsurface transport. Springs, points where the landscape and water table intersect and cold groundwater discharges, link aquifer systems with land surfaces and water bodies. As such, in many regions, they are critical to the viability of lakes, streams and cold-water fish communities. An understanding of where springs are located is important to watershed, fishery and environmental management efforts in karst regions. To better understand spatial distribution of springs and as a potential method for identifying variables that characterize locations of springs for improved land and watershed management, a nearest-neighbor analysis and a discriminant function analysis (DFA) of springs were conducted in Winona County, Minnesota, USA, a karst landscape. Nearest-neighbor analysis examined the spatial spring distribution. Twenty-two variables describing the locations of springs were analyzed to ascertain their ability to discriminate correct aquifer unit or bedrock unit classification for each spring. Springs were clumped with the highest densities in the lowest elevations. Springs were correctly assigned to aquifer units and bedrock units with eight and 11 landscape variables, respectively. Forest land cover was the only land cover type contributing to spring discrimination. Consideration of upland human activities, particularly in forested areas, on spring discharge along with a better understanding of characteristics describing spring locations could lead to better management activities that locate and protect springs and their important contributions to regional ecohydrology.

Minnesota↗

USGS1988

Distribution, status, and traditional significance of the West Indian manatee Trichechus manatus in Venezuela

Aerial and interview surveys were conducted in 1986 to determine the current distribution, status, and traditional significance of the West Indian manatee Trichechus manatus in Venezuela. Aerial surveys provided just eight tentative sightings in 73 hours of searching. These discouraging results may have been due to poor visibility, small populations, and perhaps reduced dry season manatee activity. Results of interview surveys, however, permitted a number of important generalizations. A remnant manatee population exists in Lake Maracaibo, but none occur along the more than 1500 km of Caribbean coastline. Abundance is greatest in eastern Venezuela bordering the Golfo de Paria, in the Orinoco Delta, and in the middle Orinoco and tributaries. Local market hunting in the middle of this century probably greatly reduced manatee populations in these areas. Recent protection laws, education efforts, and manatee scarcity have resulted in a declining interest in manatee hunting. Much excellent manatee habitat persists in these regions, and a continued decline in hunting could result in an optimistic outlook for future manatee populations if the incidental take in net fisheries is controlled. Traditional beliefs and legends concerning manatees in Venezuela, including hunting taboos, show that these animals remain a colorful part of the folk culture. However, manatee protection does not pose economic hardships or infringe upon traditional spiritual beliefs.

Biological Conservation↗

USGS1984

Effects of twenty-five compounds on four species of aquatic fungi (Saprolegniales) pathogenic to fish

Four species of aquatic fungi ( Achlya flagellata, A. racemosa, Saprolegnia hypogyna , and S. megasperma ) were exposed to 25 chemicals representing seven classes of compounds for 15 and 60 min, in an effort to identify potential fungicidal agents for use in fish culture. The antifungal activity of each chemical was compared with that of malachite green, a reference compound with known fungicidal properties but not registered for fishery use. Six compounds which inhibited fungal growth on artificial media at concentrations of < 100 mg/l (listed in order of decreasing antifungal activity) were the cationics Du-ter ® and copper oxychloride sulfate, the amine Lesan ® , the amide BAS-389-O1F and the cationics Cuprimyxin ® and Roccal ® II. Certain chemicals from these classes of compounds may have promise as aquatic fungicides.

Aquaculture↗

USGS1994

Detection of Aeromonas salmonicida from water using a filtration method

Aeromonas salmonicida is a principal pathogen that contributes to mortality in hatchery-maintained Atlantic salmon that originated from the Connecticut and Merrimack rivers in the northeastern United States. Field tests were conducted to assess a filtration method for detection of A. salmonicida in water used to rear fishes. A presumptive identification of typical A. salmonicida was available within 72 h and the pathogen was confirmed within 96 h. This filtration method has been incorporated into daily management practices and provides results that allowed managers to make more informed decisions for fishery resources.

Aquaculture↗

USGS1989

Impacts of exploratory drilling for oil and gas on the benthic environment of Georges Bank

A 3-year monitoring program was performed to assess the impacts of exploratory drilling for oil and gas on the benthic environment of Georges Bank, an important commercial fishery region in the North Atlantic east of Massachusetts, USA. Surficial sediments were sampled for chemical and benthic infaunal analysis and bottom still photographs were taken to document bottom microtopography and epifauna at 46 stations during 12 field surveys. The surveys were performed quarterly from just before drilling began, during drilling, and for nearly 2 years after completion of drilling. Two of the eight drilling sites were selected for monitoring. Twenty-nine stations were positioned in a tight radial array around a drilling site in 80 m of water. A second group of three stations was positioned near another drilling site in 140 m of water. The remaining stations covered a broad expanse of the Bank and adjacent suspected sites of deposition of fine-grained sediments.\ Of the 12 elements analyzed in bulk sediments, only barium increased in concentration during the period when drilling was taking place (July 1981 to September 1982). The concentration of barium in surficial sediment increased 4·7-fold from 28 ppm before drilling to 131·7 ppm after drilling at the station closest to the drilling site in 80 m of water and 5·9-fold from 32 ppm before drilling to 172 ppm after drilling at the station closest to the drilling site in 140 m of water. The concentrations of both barium and chromium increased in the fine (silt/clay) fraction (usually less than 5% by weight of sediment from most stations) of sediments from several stations around one or both rig sites monitored during the period of drilling. Elevated concentrations of chromium (about two-fold) occurred only in sediments near the drilling site in 140 m of water. Statistically significant increases in the concentration of barium in the fine fraction to sediment were detected approximately 65 km west (downcurrent) and 35 km east of the drilling site in 80 m of water after drilling was completed. The benthic fauna were abundant and diverse throughout the study area. At most stations, the dominant species remained nearly the same from one season to another over the 3 years of sampling. Polychaetes were the most abundant, followed by crustaceans. The number of individuals of some species, particularly the amphipods Erichthonius fasciatus and Unciola inermis , showed large seasonal variations. Cluster analysis revealed a strong relationship between community structure and both sediment type and water depth. Little seasonal variation was detected, but some interannual differences were revealed by cluster analysis and correspondence analysis. The replicates from a station always resembled each other more than they resembled any replicates from other stations. In addition, the combined replicates from a station always clustered with samples from that station taken on other cruises. This excellent replication and uniformity of the benthic infaunal community at a station over time made it possible to detect very subtle changes in community parameters that might be related to discharges of drilling fluid and drill cuttings. Nevertheless, no changes were detected in benthic communities of Georges Bank that could be attributed to drilling activities.

Massachusetts↗

USGS1992

Immunostimulants, adjuvants, and vaccine carriers in fish: Applications to aquaculture

Use of immunostimulants, adjuvants, and vaccine carriers in fish culture offers a wide range of attractive methods for inducing and building up protection against diseases. Immunostimulants and adjuvants can be administered before, with, or after vaccines to amplify the specific immune response generating elevations of circulating antibody titers and numbers of plaque-forming cells. Special applications of immunostimulants include assisting shower or other regimens to increase topical uptake of vaccines. In addition, immunostimulants may be used alone, inducing elevated activities in the nonspecific defense mechanisms such as increased oxidative activity of neutrophils, augmented engulfment activity of phagocytic cells, or potentiating cytotoxic cells. In cases where disease outbreaks are cyclical and can be predicted, losses may be reduced by elevating the nonspecific defense mechanisms, and the immunostimulants may be used in anticipation of events to prevent losses from diseases. Complete Freund's adjuvant was one of the first immunostimulants used in animals to elevate the specific immune response, and it has also been successfully used in conjunction with injection of fish bacterins. Other adjuvants, immunostimulants, and biological response modifiers that have been used in fisheries research include levamisole, salt baths, and bacterial lipopolysaccharides. Vaccines have been adsorbed to inert particles, such as bentonite on latex beads, to carry the immunogens to maximize in vivo uptake for bath immunization and to facilitate in vitro phagocytosis. Each substance presents special problems in timing and method of administration (injection, immersion, oral—by feed—or flush treatments), dosage adjustments for size and fish species, storage stability, and cost. An additional consideration is that the nonspecific defense mechanisms and immune responses in fish are highly variable among individuals and statistical validation requires appropriate sample numbers and carefully controlled experiments. This article reviews the literature and present concepts of use of immunostimulants, adjuvants, and vaccine carriers in fish. Cautions for use are noted, as some of these potent substances can suppress or alter biological pathways if used inappropriately. Recent research, defining pathways of the action of immunostimulants, adjuvants, and vaccine carriers, helps explain how these substances activate the protective mechanisms in fish. In addition, immunostimulants used alone hold tremendous potential for use in fish farms, hatcheries, and aquaculture facilities to reduce losses from infectious diseases. Research on the immunostimulant, levamisole, and the light oil adjuvants for use in food fish is in progress. Applications for use of these immunostimulants are proposed.

Annual Review of Fish Diseases↗

USGS1995

Viral hemorrhagic septicemia virus in North America

The first detections of viral hemorrhagic septicemia virus (VHSV) in North America were in Washington State from adult coho ( Oncorhynchus kisutch ) and chinook ( O. tshawytscha ) salmon in 1988. Subsequently, VHSV was isolated from adult coho salmon returning to hatcheries in the Pacific Northwest in 1989, 1991 and 1994. These isolates represented a strain of VHSV that was genetically different from European VHSV as determined by DNA sequence analysis and T1 ribonuclease fingerprinting. The North American strain of VHSV was also isolated from skin lesions of Pacific cod ( Gadus macrocephalus ) taken from Prince William Sound (PWS), Alaska in 1990, 1991 and 1993. In 1993 and 1994, the virus was isolated from Pacific herring ( Clupea harengus pallasi ) in Alaskan waters of PWS, Kodiak Island, Auke Bay and Port Frederick. During 1993 and 1994 the herring fishery in PWS failed from a probable complex of environmental stressors but VHSV isolates were associated with hemorrhages of the skin and fins in fish that returned to spawn. Also in 1993 and 1994, VHSV was isolated from apparently healthy stocks of herring in British Columbia, Canada and Puget Sound, Washington. Thus, the North American strain of VHSV is enzootic in the Northeastern Pacific Ocean among Pacific herring stocks with Pacific cod serving as a secondary reservoir. Although the North American strain of the virus appears to be moderately pathogenic for herring, causing occasional self-limiting epizootics, it was shown to be relatively avirulent for several species of salmonids. Pacific herring are common prey for cod and salmon and were most probably the source of the VHSV isolates from the adult salmon returning to spawn in rivers or at hatcheries in Washington State. Compelling circumstances involving the European isolates of VHSV suggest that this strain of the virus also is enzootic among marine fish in the Atlantic Oean. The highly pathogenic nature of the European strain of VHSV for salmonid fish may be the result of the exposure of rainbow trout ( O. mykiss ), an introduced species, in a stressful environment of intensive culture and the high rate of mutation inherent in all rhabdoviruses. Consequently, we recommend that efforts be made to eradicate the North American strain of VHSV when detected in live salmonids to reduce the possibility of its evolution into a more virulent salmonid virus.

Annual Review of Fish Diseases↗

USGS1993

Geological and technological assessment of artificial reef sites, Louisiana outer continental shelf

This paper describes the general procedures used to select sites for obsolete oil and gas platforms as artificial reefs on the Louisiana outer continental shelf (OCS). The methods employed incorporate six basic steps designed to resolve multiple-use conflicts that might otherwise arise with daily industry and commercial fishery operations, and to identify and assess both geological and technological constraints that could affect placement of the structures. These steps include: (1) exclusion mapping; (2) establishment of artificial reef planning areas; (3) database compilation; (4) assessment and interpretation of database; (5) mapping of geological and man-made features within each proposed reef site; and (6) site selection. Nautical charts, bathymetric maps, and offshore oil and gas maps were used for exclusion mapping, and to select nine regional planning areas. Pipeline maps were acquired from federal agencies and private industry to determine their general locations within each planning area, and to establish exclusion fairways along each pipeline route. Approximately 1600 line kilometers of high-resolution geophysical data collected by federal agencies and private industry was acquired for the nine planning areas. These data were interpreted to determine the nature and extent of near-surface geologic features that could affect placement of the structures. Seismic reflection patterns were also characterized to evaluate near-bottom sedimentation processes in the vicinity of each reef site. Geotechnical borings were used to determine the lithological and physical properties of the sediment, and for correlation with the geophysical data. Since 1987, five sites containing 10 obsolete production platforms have been selected on the Louisiana OCS using these procedures. Industry participants have realized a total savings of approximately US $1 500 000 in salvaging costs by converting these structures into artificial reefs. ?? 1993.

Ocean and Coastal Management↗

USGS2011

Bioenergetics in ecosystems

A bioenergetics model for a fish can be defined as a quantitative description of the fish’s energy budget. Bioenergetics modeling can be applied to a fish population in a lake, river, or ocean to estimate the annual consumption of food by the fish population; such applications have proved to be useful in managing fisheries. In addition, bioenergetics models have been used to better understand fish growth and consumption in ecosystems, to determine the importance of the role of fish in cycling nutrients within ecosystems, and to identify the important factors regulating contaminant accumulation in fish from lakes, rivers, and oceans.

Book chapter↗

USGS2011

Swimming and other activities: applied aspects of fish swimming performance

Human activities such as hydropower development, water withdrawals, and commercial fisheries often put fish species at risk. Engineered solutions designed to protect species or their life stages are frequently based on assumptions about swimming performance and behaviors. In many cases, however, the appropriate data to support these designs are either unavailable or misapplied. This article provides an overview of the state of knowledge of fish swimming performance – where the data come from and how they are applied – identifying both gaps in knowledge and common errors in application, with guidance on how to avoid repeating mistakes, as well as suggestions for further study.

Book chapter↗