SEARCH · Geology Reports
Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Scientists at the U.S. Geological Survey (USGS) use a range of research approaches to investigate the genetics of native and non-native species that are being managed. This Fact Sheet outlines those approaches and explains the type of information they provide.
No abstract available.
Explore the source record for details and available documents.
Functional genes and gene expression have been connected to physiological traits linked to effective production and broodstock selection in aquaculture, selective implications of commercial fish harvest, and adaptive changes reflected in non-commercial fish populations subject to human disturbance and climate change. Gene mapping using single nucleotide polymorphisms (SNPs) to identify functional genes, gene expression (analogue microarrays and real-time PCR), and digital sequencing technologies looking at RNA transcripts present new concepts and opportunities in support of effective and sustainable fisheries. Genomic tools have been rapidly growing in aquaculture research addressing aspects of fish health, toxicology, and early development. Genomic technologies linking effects in functional genes involved in growth, maturation and life history development have been tied to selection resulting from harvest practices. Incorporating new and ever-increasing knowledge of fish genomes is opening a different perspective on local adaptation that will prove invaluable in wild fish conservation and management. Conservation of fish stocks is rapidly incorporating research on critical adaptive responses directed at the effects of human disturbance and climate change through gene expression studies. Genomic studies of fish populations can be generally grouped into three broad categories: 1) evolutionary genomics and biodiversity; 2) adaptive physiological responses to a changing environment; and 3) adaptive behavioral genomics and life history diversity. We review current genomic research in fisheries focusing on those that use microarrays to explore differences in gene expression among phenotypes and within or across populations, information that is critically important to the conservation of fish and their relationship to humans.
Worldwide, in recent years capture fisheries targeting lower-trophic level forage fish and euphausiid crustaceans have been substantial (∼20 million metric tons [MT] annually). Landings of forage species are projected to increase in the future, and this harvest may affect marine ecosystems and predator-prey interactions by removal or redistribution of biomass central to pelagic food webs. In particular, fisheries targeting forage fish and euphausiids may be in competition with seabirds, likely the most sensitive of marine vertebrates given limitations in their foraging abilities (ambit and gape size) and high metabolic rate, for food resources. Lately, apparent competition between fisheries and seabirds has led to numerous high-profile conflicts over interpretations, as well as the approaches that could and should be used to assess the magnitude and consequences of fisheries-seabird resource competition. In this paper, we review the methods used to date to study fisheries competition with seabirds, and present “best practices” for future resource competition assessments. Documenting current fisheries competition with seabirds generally involves addressing two major issues: 1) are fisheries causing localized prey depletion that is sufficient to affect the birds? (i.e., are fisheries limiting food resources?), and 2) how are fisheries-induced changes to forage stocks affecting seabird populations given the associated functional or numerical response relationships? Previous studies have been hampered by mismatches in the scale of fisheries, fish, and seabird data, and a lack of causal understanding due to confounding by climatic and other ecosystem factors (e.g., removal of predatory fish). Best practices for fisheries-seabird competition research should include i) clear articulation of hypotheses, ii) data collection (or summation) of fisheries, fish, and seabirds on matched spatio-temporal scales, and iii) integration of observational and experimental (including numerical simulation) approaches to establish connections and causality between fisheries and seabirds. As no single technique can provide all the answers to this vexing issue, an integrated approach is most promising to obtain robust scientific results and in turn the sustainability of forage fish fisheries from an ecosystem perspective.
Management agencies are often charged with providing fisheries that lead to angler participation. Catch rate is one of the primary drivers of angler participation but can be influenced by a suite of factors, including population structure (e.g., density and size structure). The complexity of understanding how population structure influences angler catch rate is typified in kokanee Oncorhynchus nerka fisheries. Previous research suggests that angler catch rates of kokanee are positively influenced by fish density and total length. However, that research was based on data collected using size-selective midwater trawls. Due to the potential limitation of previous research, we sought to (1) understand the relative bias of midwater trawls and gill nets for describing the size structure of kokanee available to anglers and (2) re-evaluate the influence of fish density and fish length on angler catch rates in kokanee fisheries. Midwater trawl, gill-net, and creel data were collected on five prominent kokanee fisheries throughout Idaho in 2016 and 2017. Catch composition and percent overlap of midwater trawls, gill nets, and angler-caught fish were compared to understand the efficacy of midwater trawls and gill nets for representing the size structure of kokanee available to anglers. In addition, the influence of kokanee density and length on angler catch rates was evaluated. Midwater trawls primarily sampled small kokanee (<330 mm) and exhibited little overlap with angler-caught fish, whereas gill nets sampled more large fish (>330 mm) and exhibited higher overlap with angler-caught fish when compared to midwater trawls. Fish length was not positively associated with angler catch rates. However, fish density exhibited a positive relationship with angler catch rates. Our results highlight the importance of gear choice for understanding how kokanee populations function and elucidate the tradeoffs associated with population density, fish length, and resulting kokanee fisheries.
One of the greatest limiting factors of studies designed to obtain growth, movement, and survival in small-bodied fishes is the selection of a viable tag. The tag must be relatively small with respect to body size as to impart minimal sub-lethal effects on growth and mobility, as well as be retained throughout the life of the fish or duration of the study. Thus, body size of the model species becomes a major limiting factor; yet few studies have obtained empirical evidence of the minimum fish size and related tagging effects. The probability of surviving a tagging event was quantified in White Sands pupfish ( Cyprinodon tularosa ) across a range of sizes (19–60 mm) to address the hypothesis that body size predicts tagging survival. We compared tagging related mortality, individual taggers, growth, and tag retention in White Sands pupfish implanted with 8-mm passive integrated transponder (PIT), visual implant elastomer (VIE), and control (handled similarly, but no tag implantation) over a 75 d period. Initial body weight was a good predictor of the probability of survival in PIT- and VIE-tagged fish. As weight increased by 1 g, the fish were 4.73 times more likely to survive PIT-tag implantation compared to the control fish with an estimated suitable tagging size at 1.1 g (TL: 39.29 ± 0.41 mm). Likewise, VIE-tagged animals were 2.27 times more likely to survive a tagging event compared to the control group for every additional 1 g with an estimated size suitable for tagging of 0.9 g (TL: 36.9 ± 0.36 mm) fish. Growth rates of PIT- and VIE-tagged White Sands pupfish were similar to the control groups. This research validated two popular tagging methodologies in the White Sands pupfish, thus providing a valuable tool for characterizing vital rates in other small-bodied fishes.
Since 1921, when the first sea lamprey was recorded from Lake Erie, concern about this parasite in the Great Lakes above Niagara Falls, where previously it had never occurred, grew successively. At first, the concern was shared only in scientific circles, but as the parasite continued its persistent and rapid spread throughout the upper Great Lakes this concern was voiced by state conservation departments, the U.S. Fish and Wildlife Service, and interested fishermen. Catches of lake trout especially, and other species secondarily, began to fall below anything representing normal fluctuations in abundance. The fishing industry on Lake Huron and Lake Michigan became extremely concerned due to the fact that income was diminishing greatly. Producers on Lake Superior were fearful that the same decline in production would soon characterize their fishery.
Population availability and vessel avoidance effects on hydroacoustic abundance estimates may be scale dependent; therefore, it is important to evaluate these biases across systems. We performed an inter-ship comparison survey to determine the effect of vessel size, day-night period, depth, and environmental gradients on walleye ( Sander vitreus ) density estimates in Lake Erie, an intermediate-scaled system. Consistent near-bottom depth distributions coupled with horizontal fish movements relative to vessel paths indicated avoidance behavior contributed to higher walleye densities from smaller vessels in shallow water (i.e., <15 m), although the difference decreased with increasing depth. Diel bank migrations in response to seasonally varying onshore-to-offshore environmental gradients likely contributed to day-night differences in densities between sampling locations and seasons. Spatial and unexplained variation accounted for a high proportion of total variation; however, increasing sampling intensity can mitigate effects on precision. Therefore, researchers should minimize systematic avoidance and availability related biases (i.e., vessel and day-night period) to improve population abundance estimates. Quantifying availability and avoidance behavior effects and partitioning sources of variation provides informed flexibility for designing future hydroacoustic surveys in shallow-water nearshore environments.
The brown treesnake (BTS) invasion in Guam continues to cause extensive ecological and economic damage, yet existing control tools cannot achieve islandwide suppression or eradication, highlighting the need for new strategies. This review evaluates the feasibility of classical and genetic biocontrol approaches for BTS and identifies priority knowledge gaps. Classical biocontrol, which relies on pathogens or parasites from a pest’s native range, has had limited success in vertebrates, though certain viruses may hold potential. For BTS, prior work has identified candidate agents, including hemogregarines and paramyxoviruses, but major uncertainties remain in transmission, specificity, long term efficacy, and ecological risk. Theoretical models suggest that moderately virulent pathogens may offer the strongest potential for sustained suppression, with Ophidian paramyxoviruses emerging as a leading prospect, though substantial empirical research is still required. Genetic biocontrol offers additional possibilities, including gene drives that could bias inheritance, reduce fertility, or skew sex ratios. Self sustaining homing and shredding drives could theoretically produce long term reductions, while “enhanced” self limiting systems may provide geographically restricted alternatives. Approaches involving genetically modified prey and toxic males that shorten female lifespan through mating may have future relevance but require major development and validation. Risks across genetic strategies include unintended spread, ecological side effects, technical constraints such as producing engineered snakes, potential resistance, and regulatory complexity. Because feasibility depends on societal acceptance, the review emphasizes the need for early engagement with Guam’s local and Indigenous communities, whose perspectives will shape future development and implementation. Key research priorities include improved modeling, native range genomic characterization of BTS, expanded pathogen surveys, advances in BTS genetic tools and captive rearing methods, and further exploration of both classical pathogen candidates and genetically engineered prey systems. Collectively, the review concludes that classical and genetic biocontrol hold promise for long term, cost effective BTS suppression, but substantial scientific, ethical, ecological, and social groundwork remains before deployment.
Invasive Bighead Carp Hypophthalmichthys nobilis and Silver Carp H. molitrix have infested and caused largescale ecological and economic damage to the Illinois, Mississippi, and Ohio rivers. We compiled demographic data from 42,995 fish from 23 pools in the Illinois, Mississippi, and Ohio rivers, which universities and management agencies previously collected as part of management, monitoring, and research activities. We used this data set to test whether demographic rates (length–weight relations including body condition, mortality, growth curves, and female maturity curves) varied among subpopulations across a gradient of invasion status. We found that length–weight relations and growth curves varied among subpopulations, whereas maturity curves did not. Our findings demonstrated spatial variability in demographic rates for Bighead and Silver carp across a broad geographic area in relation to invasion status and river conditions. Herein, we provide general subpopulation management options and present different hypotheses to explain the observed spatial variability in demographic rates.
Fishing in Oklahoma’s rivers and streams provides a unique experience for anglers in the state. Despite its popularity, information on total demand and economic benefits associated with stream fishing is limited in the state. Research on the role of site quality indicators, such as fish size and quantity, on recreational fishing has shown mixed results. Whether fish size or quantity plays an important role in determining fishing demand and economic value may have important management implications. We estimated the demand and economic value of fishing under varying scenarios by using anglers’ responses to hypothetical behavioral questions related to fishing in Ozark Highland streams and rivers in Oklahoma. We asked how intended number of trips might change in the future given hypothetical increases in catch rates of fish, catch rates of trophy-sized fish, and catch rates of preferred fish species, in combination with anglers’ trip-related data. Under current conditions, we estimated consumer surplus per person per trip to be $55 and aggregate value across all stream anglers in Oklahoma to be $68.51 million. Changes in marginal benefits varied among hypothetical scenarios of fish size and abundance but was maximized with a 25% increase in catch rates of trophy-sized fish. The study findings contribute to the understanding of the economic benefit of fishing in streams and suggest that fish size, rather than fish quantity, is more important to stream anglers in the area.
Incorporation of autonomous uncrewed surface vessels (USVs) into large-scale acoustic surveys may enhance spatiotemporal extent and quality of fish density estimates. Lake Erie is currently surveyed by three motorized research vessels (RVs), which annually collect acoustic data and estimate prey-fish abundances. To evaluate the feasibility of incorporating a USV into the existing survey to increase spatial coverage, we compared paired acoustic measurements of target strength (TS), area backscattering coefficient (ABC), and areal fish density from four motorized RVs (three currently and one historically used) and one USV (Saildrone Explorer). Acoustic data were collected along 2-km transects during five sampling events distributed throughout Lake Erie. Despite observing event-specific differences that were likely impacted by sampling conditions, survey-level estimates of areal density between RVs and the USV were comparable (i.e., RV 6% lower than USV). RVs and the USV appear to react differently (speed and stability) to variable environmental conditions (wind and waves), which impacted data quality and must be mitigated in future applications. However, similar to previous comparisons in marine and freshwater environments, incorporating a USV into an acoustic survey could enhance annual fish density estimates by increasing effort, spatial coverage, logistical flexibility, and biological data collection opportunities from RVs.
Degradation of aquatic habitats has motivated construction and research on the use of artificial reefs to enhance production of fish populations. However, reefs are often poorly planned, reef design characteristics are not evaluated, and reef assessments are short-term. We constructed 29 reefs in Thunder Bay, Lake Huron, in 2010 and 2011 to mitigate for degradation of a putative lake trout spawning reef. Reefs were designed to evaluate lake trout preferences for height, orientation, and size, and were compared with two degraded natural reefs and a high-quality natural reef (East Reef). Eggs and fry were sampled on each reef for five years post-construction, and movements of 40 tagged lake trout were tracked during three spawning seasons using acoustic telemetry. Numbers of adults and spawning on the constructed reefs were initially low, but increased significantly over the five years, while remaining consistent on East Reef. Adult density, egg deposition, and fry catch were not related to reef height or orientation of the constructed reefs, but were related to reef size and adjacency to East Reef. Adult lake trout visited and spawned on all except the smallest constructed reefs. Of the metrics used to evaluate the reefs, acoustic telemetry produced the most valuable and consistent data, including fine-scale examination of lake trout movements relative to individual reefs. Telemetry data, supplemented with diver observations, identified several previously unknown natural spawning sites, including the high-use portions of East Reef. Reef construction has increased the capacity for fry production in Thunder Bay without apparently decreasing the use of the natural reef. Results of this project emphasize the importance of multi-year reef assessment, use of multiple assessment methods, and comparison of reef characteristics when developing artificial reef projects. Specific guidelines for construction of reefs focused on enhancing lake trout spawning are suggested.
The life cycle of diadromous fishes such as salmonids involves natural mortality in a series of distinct life history stages, occurring sequentially in different habitats. Decades of research have emphasized mortality at the embryo, juvenile, and sub-adult stages but it is increasingly clear that some adults that survive and return to freshwater habitats die during the final homeward migration or after they reach the spawning grounds, prior to breeding. These are termed “en route” and “prespawning” mortality, respectively, and can threaten populations depleted by mortality at previous stages. In this study, we present evidence that the sockeye salmon, Oncorhynchus nerka, population that returns to the Lake Washington Basin, in Washington State, USA, is experiencing both forms of adult mortality. Counts of the salmon entering the basin on their return migration in June and July were compared to counts in the major spawning grounds in September through November for 1995–2018. The disparity has increased markedly in recent years. The counts on the spawning grounds have decreased as a proportion of the number entering the system with an average 49 % of sockeye unaccounted for, consistent with increased en route mortality. In addition, prespawning mortality rates have increased in salmon that reach the Cedar River, the main spawning tributary, both at a hatchery holding adult fish in 1995–2018, and in the naturally spawning populations when monitored in the last five years. Hatchery records indicated <10 % prespawning mortality for 1995–2010, increasing to an average 43 % for 2014 – 2018. Recent carcass surveys in the Cedar River documented that 33.6% (2014), 22.3% (2015), 30.3% (2016) and 50.0% (2018) of female sockeye died before completing spawning. These recent increases in prespawning mortality have been associated with warm water during entry to freshwater, but comparably warm water in past decades had no such effect. Steady warming of river temperatures around the median run completion date from < 8.0 °C to > 13.0 °C was correlated with increased prespawning mortality rates at the hatchery from 1995–2018. We conclude that warming conditions during migration and spawning, in concert with other factors such as infections with pathogens, are responsible for the increased prespawning mortality of adult sockeye salmon that are high enough to threaten the population’s viability.
Anglers face constraints that influence participation and dropout rates. Some recreational anglers may be able to negotiate constraints by altering the timing or frequency of participation, acquiring new skills, or modifying nonrecreational aspects such as family or work responsibilities. We consider data collected via a mail survey from Georgia-resident trout license holders to identify both perceived constraints and strategies used to negotiate them. To capture variation among anglers, survey responses were grouped by level of angler specialization using K -means cluster analysis, which resulted in a three-cluster solution of most, moderately, and least specialized anglers. Analyses of variance were used to detect potential differences among the three specialization clusters. Tests revealed that the least specialized anglers experienced constraints more intensely than the most or moderately specialized anglers. Likewise, least specialized anglers were less able to negotiate constraints when compared to the most or moderately specialized anglers. However, the least specialized anglers used negotiation strategies involving overcoming perceived lack of skill more intensely than their counterparts. The most intensely experienced constraints overall were lack of time due to work or family obligations and distance to Georgia’s trout waters from home. The most intensely used negotiation strategies overall were “learn to enjoy being outside and stress less about catching fish” and “encourage family or friends to go fishing with me.” This research benefits fishery managers by providing a method of identifying angling groups that perceive more constraints and are less likely to overcome these constraints through constraint negotiation strategies. With this information, managers may choose to tailor efforts towards reducing constraints for angling groups that have low participation and may drop out of the activity all together.
During 21 months of sampling with various techniques, we captured 24 species of fish in Britton Reservoir. Nine species comprised over 96% of the number of fish captured and approximately 88% of the biomass. Five native non-game species accounted for over 77% of the catches. The native non-game fishes have maintained large populations in the reservoir despite continued introductions of non-native species. Two sources of non-native species exist. The first is the introduction of exotic species directly into the reservoir during fish-stocking programs. The second is the continuous movement of non-native fishes into the reservoir from large populations which reside in a major tributary of the reservoir. Factors responsible for the large number of native fishes are: management of the reservoir for hydroelectric generation; temperature regime; reservoir morphology. The fish community structure is stratified along two axes: upper basin/lower basin and inshore/offshore. Most of the 24 species were found inshore: 14 species were found offshore. Four of the native non-game fishes were most abundant in the upper basin: three introduced non-native fishes were most abundant in the lower basin of the reservoir. The offshore community was dynamic on a daily and seasonal basis.