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At least 1,045 records · Page 58Linked to original sources

USGS2000

Genetic analyses reveal unusually high diversity of infectious haematopoietic necrosis virus in rainbow trout aquaculture

Infectious haematopoietic necrosis virus (IHNV) is the most significant virus pathogen of salmon and trout in North America. Previous studies have shown relatively low genetic diversity of IHNV within large geographical regions. In this study, the genetic heterogeneity of 84 IHNV isolates sampled from rainbow trout ( Oncorhynchus mykiss ) over a 20 year period at four aquaculture facilities within a 12 mile stretch of the Snake River in Idaho, USA was investigated. The virus isolates were characterized using an RNase protection assay (RPA) and nucleotide sequence analyses. Among the 84 isolates analysed, 46 RPA haplotypes were found and analyses revealed a high level of genetic heterogeneity relative to that detected in other regions. Sequence analyses revealed up to 7·6% nucleotide divergence, which is the highest level of diversity reported for IHNV to date. Phylogenetic analyses identified four distinct monophyletic clades representing four virus lineages. These lineages were distributed across facilities, and individual facilities contained multiple lineages. These results suggest that co-circulating IHNV lineages of relatively high genetic diversity are present in the IHNV populations in this rainbow trout culture study site. Three of the four lineages exhibited temporal trends consistent with rapid evolution.

Journal of General Virology↗

USGS2025

Navigating new threats: Prey naivete in native mammals

1. Invasive predators pose a substantial threat to global biodiversity. Native prey species frequently exhibit naïveté to the cues of invasive predators, and this phenomenon may contribute to the disproportionate impact of invasive predators on prey populations. However, not all species exhibit naïveté, which has led to the generation of many hypotheses to explain patterns in prey responses. These hypotheses primarily fall into two categories: system-centric hypotheses related to biogeographic isolation (BIH) and species-centric hypotheses, like the arche type similarity hypothesis (ASH). 2. We tested the predictions of these hypotheses by assessing the response of the common raccoon ( Procyon lotor ) and hispid cotton rat ( Sigmodon hispidus ), two native mammal species with divergent snake predation histories, to the cues of the invasive Burmese python ( Python bivittatus ) in the Florida Everglades (USA). Using giving-up densities (GUDs), we assessed the responses of both cotton rats and raccoons to life-size replicas of Burmese pythons and two North American predators eastern diamondback rattlesnakes ( Crotalus adamanteus ) and coyotes ( Canis latrans ). 3. Although cotton rats increased their GUD in the presence of all three predators relative to the novel-object control, raccoons only increased their GUD in coyote treatments. 4. These results align with the predictions of the ASH but not the BIH, and mirror observed patterns of population declines in invaded areas of the Florida Everglades. 5. More broadly, our findings suggest that naïveté may contribute to the vulnerability of some species to invasive predators even in large continental systems

Florida↗

USGS2019

A temporally stratified extension of space‐for‐time Cormack–Jolly–Seber for migratory animals

Understanding drivers of temporal variation in demographic parameters is a central goal of mark‐recapture analysis. To estimate the survival of migrating animal populations in migration corridors, space‐for‐time mark–recapture models employ discrete sampling locations in space to monitor marked populations as they move past monitoring sites, rather than the standard practice of using fixed sampling points in time. Because these models focus on estimating survival over discrete spatial segments, model parameters are implicitly integrated over the temporal dimension. Furthermore, modeling the effect of time‐varying covariates on model parameters is complicated by unknown passage times for individuals that are not detected at monitoring sites. To overcome these limitations, we extended the Cormack–Jolly–Seber (CJS) framework to estimate temporally stratified survival and capture probabilities by including a discretized arrival time process in a Bayesian framework. We allow for flexibility in the model form by including temporally stratified covariates and hierarchical structures. In addition, we provide tools for assessing model fit and comparing among alternative structural models for the parameters. We demonstrate our framework by fitting three competing models to estimate daily survival, capture, and arrival probabilities at four hydroelectric dams for over 200 000 individually tagged migratory juvenile salmon released into the Snake River, USA.

Biometrics↗

USGS2013

The density dilemma: limitations on juvenile production in threatened salmon populations

Density-dependent processes have repeatedly been shown to have a central role in salmonid population dynamics, but are often assumed to be negligible for populations at low abundances relative to historical records. Density dependence has been observed in overall spring/summer Snake River Chinook salmon Oncorhynchus tshawytscha production, but it is not clear how patterns observed at the aggregate level relate to individual populations within the basin. We used a Bayesian hierarchical modelling approach to explore the degree of density dependence in juvenile production for nine Idaho populations. Our results indicate that density dependence is ubiquitous, although its strength varies between populations. We also investigated the processes driving the population-level pattern and found density-dependent growth and mortality present for both common life-history strategies, but no evidence of density-dependent movement. Overwinter mortality, spatial clustering of redds and limited resource availability were identified as potentially important limiting factors contributing to density dependence. The ubiquity of density dependence for these threatened populations is alarming as stability at present low abundance levels suggests recovery may be difficult without major changes. We conclude that density dependence at the population level is common and must be considered in demographic analysis and management.

Ecology of Freshwater Fish↗

USGS2025

Groundwater structures fish growth and production across a riverscape

Landscapes are composed of habitat patches and conditions that vary across space and time. While habitat variability and complexity can support important ecological processes and ecosystem services, the dynamic nature of habitats can also constrain organismal growth and production as optimal conditions are fleeting. In riverine ecosystems, groundwater discharge to streams stabilises water temperature and flow regimes, thus mediating how habitat complexity is expressed. Yet, how stable habitats structure growth and production within the broader landscape matrix is not well understood. In this study, we explored the effects of groundwater on spatiotemporal variation in growth and production for juvenile Yellowstone cutthroat trout ( Oncorhynchus virginalis bouvieri ) across the upper Snake River catchment, Wyoming, USA. We combined machine learning techniques and remotely sensed landscape data to estimate groundwater availability across the river network, which we linked to stream temperature regimes and conspecific density. We then used Bayesian hierarchical models to quantify the effects of temperature, density and groundwater on spatiotemporal variation in fish growth and production in 52 focal reaches. Finally, we predicted body size trajectories and trends in total production continuously over both space and time to understand the effect of groundwater at the riverscape scale. Groundwater discharged to streams where topography changes abruptly in valley-bottom areas underlain by coarse glacial deposits. Groundwater stabilised temperature regimes and was associated with high trout densities. Temperature and density, in turn, interacted to influence growth rates: growth increased strongly with temperature, but this effect was reduced when density was high. Accordingly, variation in groundwater availability among stream reaches diversified growth and production regimes. In reaches with low groundwater availability, growth and production declined over time from summer maxima. In contrast, in reaches with high groundwater availability, temporal trends in growth and production were hump-shaped—peaking in autumn—and mean production was greater. At the riverscape scale, temporal asynchrony in growth rates generated convergent spatial variation in growth capacity, but—when combined with density—led to the formation of distinct hotspots of production. Our results demonstrate how groundwater, an important driver of aquatic ecosystem heterogeneity, structures trout growth and production across space and time. Importantly, rare, but stable habitats may disproportionately affect ecological processes and serve as key sources of population diversity at larger spatial scales.

Wyoming↗

USGS2013

Ambient changes in tracer concentrations from a multilevel monitoring system in Basalt

Starting in 2008, a 4-year tracer study was conducted to evaluate ambient changes in groundwater concentrations of a 1,3,6-naphthalene trisulfonate tracer that was added to drill water. Samples were collected under open borehole conditions and after installing a multilevel groundwater monitoring system completed with 11 discrete monitoring zones within dense and fractured basalt and sediment layers in the eastern Snake River aquifer. The study was done in cooperation with the U.S. Department of Energy to test whether ambient fracture flow conditions were sufficient to remove the effects of injected drill water prior to sample collection. Results from thief samples indicated that the tracer was present in minor concentrations 28 days after coring, but was not present 6 months after coring or 7 days after reaming the borehole. Results from sampling the multilevel monitoring system indicated that small concentrations of the tracer remained in 5 of 10 zones during some period after installation. All concentrations were several orders of magnitude lower than the initial concentrations in the drill water. The ports that had remnant concentrations of the tracer were either located near sediment layers or were located in dense basalt, which suggests limited groundwater flow near these ports. The ports completed in well-fractured and vesicular basalt had no detectable concentrations.

Idaho↗

USGS2009

Behavioural thermoregulation by subyearling fall (autumn) Chinook salmon oncorhynchus tshawytscha in a reservoir

This study investigated behavioural thermoregulation by subyearling fall (autumn) Chinook salmon Oncorhynchus tshawytscha in a reservoir on the Snake River, Washington, U.S.A. During the summer, temperatures in the reservoir varied from 23?? C on the surface to 11?? C at 14 m depth. Subyearlings implanted with temperature-sensing radio transmitters were released at the surface at temperatures >20?? C during three blocks of time in summer 2004. Vertical profiles were taken to measure temperature and depth use as the fish moved downstream over an average of 5??6-7??2 h and 6??0-13??8 km. The majority of the subyearlings maintained average body temperatures that differed from average vertical profile temperatures during most of the time they were tracked. The mean proportion of the time subyearlings tracked within the 16-20?? C temperature range was larger than the proportion of time this range was available, which confirmed temperature selection opposed to random use. The subyearlings selected a depth and temperature combination that allowed them to increase their exposure to temperatures of 16-20?? C when temperatures <16 and >20?? C were available at lower and higher positions in the water column. A portion of the subyearlings that selected a temperature c. 17??0?? C during the day, moved into warmer water at night coincident with an increase in downstream movement rate. Though subyearlings used temperatures outside of the 16-20?? C range part of the time, behavioural thermoregulation probably reduced the effects of intermittent exposure to suboptimal temperatures. By doing so, it might enhance growth opportunity and life-history diversity in the population of subyearlings studied.

Journal of Fish Biology↗

USGS2011

Lithosphere-asthenosphere interaction beneath the western United States from the joint inversion of body-wave traveltimes and surface-wave phase velocities

The relation between the complex geological history of the western margin of the North American plate and the processes in the mantle is still not fully documented and understood. Several pre-USArray local seismic studies showed how the characteristics of key geological features such as the Colorado Plateau and the Yellowstone Snake River Plains are linked to their deep mantle structure. Recent body-wave models based on the deployment of the high density, large aperture USArray have provided far more details on the mantle structure while surface-wave tomography (ballistic waves and noise correlations) informs us on the shallow structure. Here we combine constraints from these two data sets to image and study the link between the geology of the western United States, the shallow structure of the Earth and the convective processes in mantle. Our multiphase DNA10-S model provides new constraints on the extent of the Archean lithosphere imaged as a large, deeply rooted fast body that encompasses the stable Great Plains and a large portion of the Northern and Central Rocky Mountains. Widespread slow anomalies are found in the lower crust and upper mantle, suggesting that low-density rocks isostatically sustain part of the high topography of the western United States. The Yellowstone anomaly is imaged as a large slow body rising from the lower mantle, intruding the overlying lithosphere and controlling locally the seismicity and the topography. The large E-W extent of the USArray used in this study allows imaging the 'slab graveyard', a sequence of Farallon fragments aligned with the currently subducting Juan de Fuca Slab, north of the Mendocino Triple Junction. The lithospheric root of the Colorado Plateau has apparently been weakened and partly removed through dripping. The distribution of the slower regions around the Colorado Plateau and other rigid blocks follows closely the trend of Cenozoic volcanic fields and ancient lithospheric sutures, suggesting that the later exert a control on the locus of magmato-tectonic activity today. The DNA velocity models are available for download and slicing at http://dna.berkeley.edu. ?? 2011 The Authors Geophysical Journal International ?? 2011 RAS.

Geophysical Journal International↗

USGS2010

Invasive reptiles and amphibians: global perspectives and local solutions

In the annals of invasive species biology, higher taxa such asmammals, plants and insects have received the lion’s shareof research attention, largely because many of these invadershave demonstrated a remarkable ability to degrade ecosys-tems and cause economic harm. Interest in invasive reptilesand amphibians (collectively ‘herpetofauna’, colloquially‘herps’) has historically lagged but is now garnering in-creased scrutiny as a result of their escalating pace ofinvasion. A few herpetofaunal invaders have received con-siderable attention in scientiﬁc and popular accounts, in-cluding the brown treesnakeBoiga irregularison Guam,Burmese pythonPython molurusin Florida, Coqu´ıEleutherodactylus coquiin Hawaii and cane toadBufomarinusin Australia. However, relatively few are aware ofmany emerging and potentially injurious herpetofaunalinvaders, such as Nile monitorsVaranus niloticusin Flor-ida, common kingsnakesLampropeltis getulain the CanaryIslands, boa constrictorsBoa constrictoron Aruba andCozumel, or a variety of giant constrictor snakes in PuertoRico. For the vast majority of the most commonlyintroduced species, real or potential impacts to nativeecosystems or human economic interests are poorly under-stood and incompletely explored; major pathways of intro-duction have only recently been elucidated, and effectivemanagement interventions have been limited (Kraus, 2009).

Animal Conservation↗

USGS2006

Comparison of methods for estimating ground-water pumpage for irrigation

Ground-water pumpage for irrigation was measured at 32 sites on the eastern Snake River Plain in southern Idaho during 1983. Pumpage at these sites also was estimated by three commonly used methods, and pumpage estimates were compared to measured values to determine the accuracy of each estimate. Statistical comparisons of estimated and metered pumpage using an F-test showed that only estimates made using the instantaneous discharge method were not significantly different (α. = 0.01) from metered values. Pumpage estimates made using the power consumption method reflect variability in pumping efficiency among sites. Pumpage estimates made using the crop-consumptive use method reflect variability in water-management practices. Pumpage estimates made using the instantaneous discharge method reflect variability in discharges at each site during the irrigation season.

Groundwater↗

USGS2012

Ecological correlates of invasion impact for Burmese pythons in Florida

An invasive population of Burmese pythons ( Python molurus bivittatus ) is established across several thousand square kilometers of southern Florida and appears to have caused precipitous population declines among several species of native mammals. Why has this giant snake had such great success as an invasive species when many established reptiles have failed to spread? We scored the Burmese python for each of 15 literature-based attributes relative to predefined comparison groups from a diverse range of taxa and provide a review of the natural history and ecology of Burmese pythons relevant to each attribute. We focused on attributes linked to spread and magnitude of impacts rather than establishment success. Our results suggest that attributes related to body size and generalism appeared to be particularly applicable to the Burmese python's success in Florida. The attributes with the highest scores were: high reproductive potential, low vulnerability to predation, large adult body size, large offspring size and high dietary breadth. However, attributes of ectotherms in general and pythons in particular (including predatory mode, energetic efficiency and social interactions) might have also contributed to invasion success. Although establishment risk assessments are an important initial step in prevention of new establishments, evaluating species in terms of their potential for spreading widely and negatively impacting ecosystems might become part of the means by which resource managers prioritize control efforts in environments with large numbers of introduced species.

Florida↗

USGS2007

Ground water in perspective

Owing to their enormous capacity, ground‐water reservoirs are at least equal in importance to the ground water itself. As regulators of water movement in the hydrological cycle, these reservoirs surpass all lakes combined, natural and manmade. While many aquifers are not well understood, data on many others are adequate for long‐range broad‐scale planning. An example is the basalt aquifer of the Snake River Plain in Idaho. However, the area has managerial problems which concern the time, the place and the feasibility of manipulations of water. All continents of the world contain great aquifers. For every huge aquifer, however, hundreds of smaller ones occur, and even these contain astonishing amounts of water. Aquifers in the Ohio River Basin of the United States are good examples. Management of total water resources is a difficult problem at many places. But many problems could be met and many water shortages alleviated or eliminated by use of aquifers, not merely as sources of water, but as reservoirs for management of water.

Idaho, Wyoming, Montana, Oregon↗

USGS2017

Status of White Sturgeon (Acipenser transmontanus Richardson, 1863) throughout the species range, threats to survival, and prognosis for the future

White Sturgeon, Acipenser transmontanus (WS), are distributed throughout three major river basins on the West Coast of North America: the Sacramento-San Joaquin, Columbia, and Fraser River drainages. Considered the largest North American freshwater fish, some WS use estuarine habitat and make limited marine movements between river basins. Some populations are listed by the United States or Canada as threatened or endangered (upper Columbia River above Grand Coulee Dam; Kootenai River; lower, middle and, upper Fraser River and Nechako River), while others do not warrant federal listing at this time (Sacramento-San Joaquin Rivers; Columbia River below Grand Coulee Dam; Snake River). Threats that impact WS throughout the species’ range include fishing effects and habitat alteration and degradation. Several populations suffer from recruitment limitations or collapse due to high early life mortality associated with these threats. Efforts to preserve WS populations include annual monitoring, harvest restrictions, habitat restoration, and conservation aquaculture. This paper provides a review of current knowledge on WS life history, ecology, physiology, behavior, and genetics and presents the status of WS in each drainage. Ongoing management and conservation efforts and additional research needs are identified to address present and future risks to the species.

Journal of Applied Ichthyology↗

USGS2014

The behavioural response of adult Petromyzon marinus to damage-released alarm and predator cues

Using semi‐natural enclosures, this study investigated (1) whether adult sea lamprey Petromyzon marinus show avoidance of damage‐released conspecific cues, damage‐released heterospecific cues and predator cues and (2) whether this is a general response to injured heterospecific fishes or a specific response to injured P. marinus . Ten replicate groups of 10 adult P. marinus , separated by sex, were exposed to one of the following nine stimuli: deionized water (control), extracts prepared from adult P. marinus , decayed adult P. marinus (conspecific stimuli), sympatric white sucker Catostomus commersonii , Amazon sailfin catfish Pterygoplichthys pardalis (heterospecific stimuli), 2‐phenylethylamine (PEA HCl) solution, northern water snake Nerodia sipedon washing, human saliva (predator cues) and an adult P. marinus extract and human saliva combination (a damage‐released conspecific cue and a predator cue). Adult P. marinus showed a significant avoidance response to the adult P. marinus extract as well as to C. commersonii , human saliva, PEA and the adult P. marinus extract and human saliva combination. For mobile P. marinus , the N. sipedon washing induced behaviour consistent with predator inspection. Exposure to the P. pardalis extract did not induce a significant avoidance response during the stimulus release period. Mobile adult female P. marinus showed a stronger avoidance behaviour than mobile adult male P. marinus in response to the adult P. marinus extract and the adult P. marinus extract and human saliva combination. The findings support the continued investigation of natural damage‐released alarm cue and predator‐based repellents for the behavioural manipulation of P. marinus populations in the Laurentian Great Lakes.

Journal of Fish Biology↗

USGS2014

Fatty-acid profiles of white muscle and liver in stream-maturing steelhead trout Oncorhynchus mykiss from early migration to kelt emigration

The profiles of specific fatty acids (FA) in white muscle and liver of fasting steelhead trout Oncorhynchus mykiss were evaluated at three periods during their prespawning migration and at kelt emigration in the Snake–Columbia River of Washington, Oregon and Idaho, to improve the understanding of energy change. Twenty-seven FAs were identified; depletion of 10 of these was positively correlated in liver and white muscle of prespawning O. mykiss . To observe relative changes in FA content more accurately over sampling intervals, the lipid fraction of tissues was used to normalize the quantity of individual FA to an equivalent tissue wet mass. Saturated and monounsaturated FAs were depleted between upstream migration in September and kelt emigration in June, whereas polyunsaturated FAs were more conserved. Liver was depleted of FAs more rapidly than muscle. Three FAs were detected across all sampling intervals: 16:0, 18:1 and 22:6n3, which are probably structurally important to membranes. When structurally important FAs of O. mykiss are depleted to provide energy, physiological performance and survival may be affected.

Montana, Oregon, Washington↗

USGS2023

Timing of reproduction underlies fitness tradeoffs for a salmonid fish

Life history diversity is generated and maintained in part by density-dependent fitness tradeoffs that inhibit a single trait value from reaching fixation. While central to our understanding of evolution, demonstrating density dependence in the strength of fitness tradeoffs is difficult in natural systems. The timing of reproduction is a key life history trait that determines access to breeding habitat and exposure of offspring to competitive interactions and environmental conditions. Understanding the processes underlying diversity in reproductive timing will aid efforts to increase adaptive capacity under global environmental change. Here, we used detailed field studies, genetic parentage assignment, and simulation modeling to evaluate the fitness tradeoffs associated with the timing of reproduction for Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri in groundwater-dominated tributaries to the upper Snake River, Wyoming, USA. We conducted our study across two years to understand how the strength of tradeoffs changes with population density. We found that early breeders experienced reduced reproductive success relative to later breeders due to the negative impact of nest superimposition (where later breeders construct nests overlapping those constructed previously) on embryo survival. However, as the risk of superimposition declined in the low-density year and early breeders experienced fewer losses, reproductive success became more similar among individuals breeding at different times. Further, in the spring following the critical period for growth and survival, offspring of early breeders had experienced longer growing seasons, attained larger body sizes, and were equally abundant relative to those of later breeders, suggesting that fitness losses due to superimposition may be offset by size-dependent competitive ability and overwinter survival. Our results illustrate a mechanism underlying diversity in the timing of reproduction for salmonids. This type of life history diversity will help to ensure the resilience and stability of salmonid populations attempting to adapt to changing local stressors associated with global climate change.

Oikos↗

USGS1975

Magma beneath Yellowstone National Park

The Yellowstone plateau volcanic field is less than 2 million years old, lies in a region of intense tectonic and hydrothermal activity, and probably has the potential for further volcanic activity. The youngest of three volcanic cycles in the field climaxed 600,000 years ago with a voluminous ashflow eruption and the collapse of two contiguous cauldron blocks. Doming 150,000 years ago, followed by voluminous rhyolitic extrusions as recently as 70,000 years ago, and high convective heat flow at present indicate that the latest phase of volcanism may represent a new magmatic insurgence. These observations, coupled with (i) localized postglacial arcuate faulting beyond the northeast margin of the Yellowstone caldera, (ii) a major gravity low with steep bounding gradients and an amplitude regionally atypical for the elevation of the plateau, (iii) an aeromagnetic low reflecting extensive hydrothermal alteration and possibly indicating the presence of shallow material above its Curie temperature, (iv) only minor shallow seismicity within the caldera (in contrast to a high level of activity in some areas immediately outside), (v) attenuation and change of character of seismic waves crossing the caldera area, and (vi) a strong azimuthal pattern of teleseismic P-wave delays, strongly suggest that a body composed at least partly of magma underlies the region of the rhyolite plateau, including the Tertiary volcanics immediately to its northeast. The Yellowstone field represents the active end of a system of similar volcanic foci that has migrated progressively northeastward for 15 million years along the trace of the eastern Snake River Plain. Regional aeromagnetic patterns suggest that this course was guided by the structure of the Precambrian basement. If, as suggested by several investigators, the Yellowstone magma body marks a contemporary deep mantle plume, this plume, in its motion relative to the North American plate, would appear to be "navigating" along a fundamental structure in the relatively shallow and brittle lithosphere overhead. The concept that a northeastward-propagating major crustal fracture controls the migration path of the major foc

Wyoming↗

USGS2004

Complete genome sequence of Fer-de-Lance Virus reveals a novel gene in reptilian Paramyxoviruses

The complete RNA genome sequence of the archetype reptilian paramyxovirus, Fer-de-Lance virus (FDLV), has been determined. The genome is 15,378 nucleotides in length and consists of seven nonoverlapping genes in the order 3??? N-U-P-M-F-HN-L 5???, coding for the nucleocapsid, unknown, phospho-, matrix, fusion, hemagglutinin-neuraminidase, and large polymerase proteins, respectively. The gene junctions contain highly conserved transcription start and stop signal sequences and tri-nucleotide intergenic regions similar to those of other Paramyxoviridae. The FDLV P gene expression strategy is like that of rubulaviruses, which express the accessory V protein from the primary transcript and edit a portion of the mRNA to encode P and I proteins. There is also an overlapping open reading frame potentially encoding a small basic protein in the P gene. The gene designated U (unknown), encodes a deduced protein of 19.4 kDa that has no counterpart in other paramyxoviruses and has no similarity with sequences in the National Center for Biotechnology Information database. Active transcription of the U gene in infected cells was demonstrated by Northern blot analysis, and bicistronic N-U mRNA was also evident. The genomes of two other snake paramyxovirus genotypes were also found to have U genes, with 11 to 16% nucleotide divergence from the FDLV U gene. Pairwise comparisons of amino acid identities and phylogenetic analyses of all deduced FDLV protein sequences with homologous sequences from other Paramyxoviridae indicate that FDLV represents a new genus within the subfamily Paramyxovirinae. We suggest the name Ferlavirus for the new genus, with FDLV as the type species.

Journal of Virology↗