Salmonid fish raised in hatcheries often have lower fitness (number of returning adult offspring) than wild fish when both spawn in the wild. Body size at release from hatcheries is positively correlated with survival at sea. So one explanation for reduced fitness is that hatcheries inadvertently select for trait values...
Plasmid transformation of chlamydiae has created new opportunities to investigate host–microbe interactions during chlamydial infections; however, there are still limitations. Plasmid transformation requires a replicon derived from the native Chlamydia plasmid, and these transformations are species-specific. We explored the utility of a broad host-range plasmid, pBBR1MCS-4, to transform chlamydiae, with...
Plasma biochemistry and hematology reference intervals are integral health assessment tools in all medical fields, including aquatic animal health. As sablefish (Anoplopoma fimbria) are becoming aquaculturally and economically more important, this manuscript provides essential reference intervals (RI) for their plasma biochemistry and hematology along with reference photomicrographs of blood cells...
Phytoplankton samples were collected from 5 upper Willamette Basin reservoirs in variable months during years 2013-2016 and 2019. Samples were collected from Blue River Reservoir, Cougar Reservoir, Fall Creek Reservoir, Lookout Point Reservoir, and Hills Creek Reservoir. The phytoplankton were identified and enumerated by Jim Sweet at Aquatic Analysts. Density...
Water chemistry measurements taken at or downstream of Fall Creek Reservoir, OR (43.9459714, -122.755765). Fall Creek is a tributary of the Middle Fork Willamette River, located approximately 20 miles SE of Eugene, Oregon, USA.
Water chemistry measurements included water samples collected from the reservoir outflow (during autumn drawdown) and within...
This dataset accompanies the manuscript Unintended consequences of selective water withdrawals from reservoirs alter downstream macroinvertebrate communities in Water Resources Research.
Benthic macroinvertebrates were collected from samples taken annually during the first two weeks of August from 2002-2007 and again in 2017 at six sites in the South Fork McKenzie...
This dataset consists of vascular plant species cover estimates collected from 12, 1x1-m quadrats, nested within 15x15-m plots that excluded and were open to wild ungulate access. The wild ungulate exclusion experiment was conducted in young forest plantations (<6 years old), each randomly assigned to one of 3 silvicultural herbicide...
We studied avian development in 49 species of temperate and 153 species of tropical New World passerine birds to determine how growth rates, and incubation and nestling periods, varied in relation to other life-history traits. We collected growth data and generated unbiased mass and tarsus growth rate estimates (mass n...
To investigate the effects of logging, three small watersheds in the Alsea River basin on the west slope of the Oregon Coast Range were selected for study. This was an interdisciplinary investigation to evaluate the influence of specific logging methods on stream regimen and on aquatic resources. The study plan...
This dataset is based on quantitative PCR (qPCR) output. Output from all qPCR was compiled in this dataset and kept as the original. Information about sampling time, id, concentration, sites and a conversion of the quantity in femtograms were added as complement to the qPCR output to facilitate data analysis
This data contains results from direct numerical simulations of three-dimensional, premixed, hydrogen/air flames, using the mixture-averaged diffusion model. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated article.
This data contains results from direct numerical simulations of three-dimensional, premixed, hydrogen/air flames, using the multicomponent diffusion model. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated article.
This dataset contains data layers used and produced by a fuzzy logic model for biomass loss risk under projected climate change in Oregon and Washington west of the Cascade Mountains crest.
Engineered log jams (ELJs) are commonly implemented in rivers to stabilize streambanks and diversify fish habitat, but few studies have verified the hydraulic benefits of ELJs by assessing their effects on the flow field. This field and modeling study assessed the effects of an ELJ on various characteristics of the...
Dendrochronological data provides insight in the tree development, and used in conjunction with forest inventory, can supply inputs for growth and yield modeling. However, accurate and precise measurements of a large number of incremental cores require significant resources. One possible source of valuable tree ring data are national forest inventories...
Movement in an important component of an animal’s life cycle when it relies on both aquatic and terrestrial habitats. When multiple species overlap in the use of these habitats, they rely on other methods to reduce competition for shared resources. This dataset measured the jumping performance and movement behavior of...
The accessions used in this study were comprised of 246 snap bean and 49 dry bean genotypes. Of these, 150 snap bean accessions came from the Common Bean Coordinated Agriculture Project Snap Bean Diversity panel, an assemblage of 59 Chinese snap bean genotypes obtained from a trip to China in...
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide...
Because studies of forestry effects on wetlands have been so infrequent in the Pacific Northwest, each section in this report drew heavily from studies of forestry impacts to streams and riparian zones. After assembly and synthesis, that information was extrapolated, mostly in the form of hypotheses, to the very different...
Greater sage-grouse Centrocercus urophasianus populations across North America have been declining due to degradation and fragmentation of sagebrush habitat. As part of a study quantifying greater sage-grouse demographics prior to construction of a wind energy facility, we estimated apparent net nest productivity and survival rate of chicks associated with radio-equipped...
During July 1970, albacore boats trolling surface jigs (jig boats) had record catches in an area off the mouth of the Columbia River. The jig fishery declined suddenly in late July and was poor throughout the remainder of the summer. No obvious oceanographic changes were correlated with these drastic changes...
The quantification and description of sea surface temperature (SST) is critically important because it can influence the distribution, migration, and invasion of marine species; furthermore, SSTs are expected to be affected by climate change. To better understand present temperature regimes, we assembled a 29-year nearshore time series of mean monthly...
In the face of dramatic declines in groundfish populations and a lack of sufficient stock assessment information, a need has arisen for new methods of assessing groundfish populations. We describe the integration of seafloor transect data gathered by a manned submersible with high-resolution sonar imagery to produce a habitat- based...
We form a new data set of fields of sea level anomalies by combining gridded daily fields derived from altimeter data with coastal tide gauge data. Within approximately 50-80 km of the coast, the altimeter data are discarded and replaced by a linear interpolation between the tide gauge and remaining...
This dataset was used to determine the attenuation of an audio signal by reticulated foam samples that span the natural range of intrinsic permeability for seasonal snow. Data are audio measurements acquired on a two-channel oscilloscope.
The HIV pandemic continues to impose enormous morbidity, mortality and economic burdens across the globe. Simultaneously, innovations in antiretroviral therapy, diagnostic approaches and vaccine development are providing novel tools for treatment-as-prevention and prophylaxis. We developed a mathematical model to evaluate the added benefit of an HIV vaccine in the context...
Dams impound the majority of rivers and provide important societal benefits, especially daily water releases that enable on-peak hydroelectricity generation. Such “hydropeaking” is common worldwide, but its downstream impacts remain unclear. We evaluated the response of aquatic insects, a cornerstone of river food webs, to hydropeaking using a life history–hydrodynamic...
To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of...
Dual-axis accelerometer global positioning system collars can be used to remotely record the activity level and behavior of free-ranging animals, but inter- and intraspecific variations in motion among behaviors necessitate calibration for each species of interest. To date, little work has been done to determine the best duration for sampling...
Grass carp Ctenopharyngodon idella are sometimes used as a biological tool for managing aquatic vegetation in reservoirs. Sterile, triploid fish were stocked in Devils Lake, Oregon, during 1986, 1987, and 1993 to control aquatic vegetation. We present a case study for using multiple measures on the same fish to determine...
Host resistance, both quantitative and qualitative, is the preferred long-term approach for disease management in many pathosystems, including powdery mildew of hop (Podosphaera macularis). In 2012, an epidemic of powdery mildew occurred in Washington and Idaho on previously resistant cultivars whose resistance was putatively based on the gene designated R6....
Grassland and shrubland birds are declining globally due in part to anthropogenic habitat modification. Because population performance of these species is also influenced by non-anthropogenic factors, it is important to incorporate all relevant ecological drivers into demographic models. We used design-based sampling and occupancy models to test relationships of environmental...
Sexually size-dimorphic species must show some difference between the sexes in growth rate and/or length of growing period. Such differences in growth parameters can cause the sexes to be impacted by environmental variability in different ways, and understanding these differences allows a better understanding of patterns in productivity between individuals...
Coastal upwelling regimes are some of the most productive ecosystems in the ocean but are also among the most vulnerable to ocean acidification (OA) due to naturally high background concentrations of CO₂. Yet our ability to predict how these ecosystems will respond to additional CO₂ resulting from anthropogenic emissions is...
The Bering Sea and Gulf of Alaska support a number of commercially important flatfish fisheries. These high latitude ecosystems are predicted to be most immediately impacted by ongoing ocean acidification, but the range of responses by commercial fishery species has yet to be fully explored. In this study, we examined...
These data were used to estimate the land values that enter into the Land-Use Transitions modeling component of Willamette Envision, the computer model developed by the Willamette Water 2100 Project. The land values were collected for randomly drawn samples of developed, agricultural, and forest land parcels in Benton, Lane, Marion,...
These data were collected using a survey of a sample of farmers in the Willamette Valley. The objective was to estimate a relationship between the decision to irrigate a field (one with an existing irrigation water right), and factors such as land characteristics, climate, current weather, and market prices. The...
This paper explores the development of biomechanical models for evaluating a new class of passive mechanical implants for orthopedic surgery. The proposed implants take the form of passive engineered mechanisms, and will be used to improve the functional attachment of muscles to tendons and bone by modifying the transmission of...
Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The...
This document is a report on a survey of Alsea River done with the intent to determine how best to remove obstructions to make it easier for boats to pass through.
Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native...
The trophic habits, size and condition of yearling Chinook salmon (Oncorhynchus tshawytscha) caught early in their marine residence were examined during 19 survey years (1981–1985; 1998–2011). Juvenile salmon consumed distinct highly piscivorous diets in cold and warm ocean regimes with major differences between ocean regimes driven by changes in consumption...
A steam distillation extraction kinetics experiment was conducted to estimate essential oil yield, composition, antimalarial, and antioxidant capacity of cumin (Cuminum cyminum L.) seed (fruits). Furthermore, regression models were developed to predict essential oil yield and composition for a given duration of the steam distillation time (DT). Ten DT durations...
Correction
23 Dec 2015: The PLOS ONE Staff (2015) Correction: Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders. PLOS ONE 10(12): e0145899. https://doi.org/10.1371/journal.pone.0145899
Studies of anthropogenic impacts on wildlife may produce inconclusive or biased results if they fail to account for natural sources of variation in breeding performance and do not use probabilistic sampling at a scale functional for management. We used stratified random sampling and generalized linear mixed models to test hypotheses...
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data...
This dataset contains trace-element data, descriptive information, and photographs for 328 field clays sampled in the Valley of Oaxaca, Mexico; mineralogical data are presented for a subset of the samples. The clay samples were generated as part of a valley-wide sampling strategy designed to capture spatial variation in clay composition...
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the...
Real-time PCR assays using locked nucleic acid (LNA) probes and high resolution melt (HRM) analysis were developed for molecular differentiation of Pseudoperonospora cubensis and P. humuli, causal agents of cucurbit and hop downy mildew, respectively. The assays were based on a previously identified single nucleotide polymorphism (SNP) in the cytochrome...
The diverse predatory rockfishes (Sebastes spp.) support extensive commercial fisheries in the northeastern Pacific. Although 106 species of Sebastes are considered valid, many of the ecological, geographical, and morphological boundaries separating them lack clarity. We clarify one such boundary by separating the blue rockfish Sebastes mystinus (Jordan and Gilbert, 1881)...
Motivation:
Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of...
Cymbopogon flexuosus, lemongrass, and C. martinii, palmarosa, are perennial grasses grown to produce essential oils for the fragrance industry. The objectives of this study were (1) to evaluate biomass and oil yields as a function of nitrogen and sulfur fertilization, and (2) to characterize their utility for lignocellulosic ethanol compared...
In Kentucky bluegrass (Poa pratensis), Claviceps purpurea, the causal agent of ergot, typically releases ascospores during the early-morning hours, between about midnight and 10:00 A.M., corresponding to time of flowering, when the unfertilized ovaries are most susceptible to infection. During aeromycology studies of C. purpurea in perennial ryegrass (Lolium perenne)...
This dataset supports a research project and paper where we define criteria for assessing the effectiveness of data sharing, under the assumption that the goal of data sharing is to make the data usable, with minimal effort, to the new user. We take the position that the bar should be...
Optimum timing and use of fungicides for disease control are improved by an understanding of the characteristics of fungicide physical mode of action. Greenhouse and field experiments were conducted to quantify and model the duration of pre- and postinfection activity of fungicides most commonly used for control of hop downy...
Results of 28 field trials conducted over a 12-year period investigating management of hop powdery mildew caused by Podosphaera macularis were quantitatively summarized by meta-analysis to compare product efficacy and use patterns by mode of action as defined by Fungicide Resistance Action Committee (FRAC) groups. Availability of original observations enabled...
The distribution and range of lesser prairie-chicken (Tympanuchus pallidicinctus) has been reduced by >90% since European settlement of the Great Plains of North America. Currently, lesser prairie-chickens occupy 3 general vegetation communities: sand sagebrush (Artemisia filifolia), sand shinnery oak (Quercus havardii), and mixed-grass prairies juxtaposed with Conservation Reserve Program grasslands....
Land use and climate change occur simultaneously around the globe. Fully understanding their separate and combined effects requires a mechanistic understanding at the local scale where their effects are ultimately realized. Here we applied an individual-based model of fish population dynamics to evaluate the role of local stream variability in...
We form a new data set of fields of sea level anomalies by combining gridded daily fields derived from altimeter data with coastal tide gauge data. Within approximately 50-80 km of the coast, the altimeter data are discarded and replaced by a linear interpolation between the tide gauge and remaining...
Stream-dwelling species in the U.S. southern Appalachian Mountains region are particularly vulnerable to climate change and acidification. The objectives of this study were to quantify the spatial extent of contemporary suitable habitat for acid- and thermally sensitive aquatic species and to forecast future habitat loss resulting from expected temperature increases...
Background: Arsenic is an immunotoxicant. Clinical reports observe the reactivation of varicella zoster virus (VZV) in people who have recovered from arsenic poisoning and in patients with acute promyelocytic leukemia that have been treated with arsenic trioxide. Objective: We evaluated the association between arsenic and the seroprevalence of VZV IgG...
A number of researchers have attempted to estimate salmonid smolt survival during outmigration through an estuary. However, it is currently unclear how the design of such studies influences the accuracy and precision of survival estimates. In this simulation study we consider four patterns of smolt survival probability in the estuary,...
Understanding seasonal migration and localized persistence of populations is critical for effective species harvest and conservation management. Pacific salmon (genus Oncorhynchus) forecasting models predict stock composition, abundance, and distribution during annual assessments of proposed fisheries impacts. Most models, however, fail to account for the influence of biophysical factors on year-to-year...
The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
Knowledge of processes leading to crop damage is central to devising rational approaches to disease management. Multiple experiments established that infection of hop cones by Podosphaera macularis was most severe if inoculation occurred within 15 to 21 days after bloom. This period of infection was associated with the most pronounced...
A recent identification of the two-component aggregation pheromone of the invasive stink bug species, Halyomorpha halys (Stal), in association with a synergist, has greatly improved the ability to accurately monitor the seasonal abundance and distribution of this destructive pest. We evaluated the attraction of H. halys to black pyramid traps...
Environmental contributions to cancer development are widely accepted, but only a fraction of all pertinent exposures have probably been identified. Traditional toxicological approaches to the problem have largely focused on the effects of individual agents at singular endpoints. As such, they have incompletely addressed both the pro-carcinogenic contributions of environmentally...
Upriver movements were determined for Chinook salmon Oncorhynchus tshawytscha returning to the Yukon River, a large, virtually pristine river basin. These returns have declined dramatically since the late 1990s, and information is needed to better manage the run and facilitate conservation efforts. A total of 2,860 fish were radio tagged...
For widely distributed species at risk, such as Pacific salmon (Oncorhynchus spp.), habitat monitoring is both essential and challenging. Only recently have widespread monitoring programs been implemented for salmon habitat in the Pacific Northwest. Remote sensing data, such as Landsat images, are therefore a useful way to evaluate trends prior...
Pursuit of the triple bottom line of economic, community and ecological sustainability has increased the complexity of fishery management; fisheries assessments require new types of data and analysis to guide science-based policy in addition to traditional biological information and modeling. We introduce the Fishery Performance Indicators (FPIs), a broadly applicable...
Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02' S) to Chiloé...
We inferred the population densities of blue whales (Balaenoptera musculus) and short-beaked common dolphins (Delphinus delphis) in the Northeast Pacific Ocean as functions of the water-column’s physical structure by implementing hierarchical models in a Bayesian framework. This approach allowed us to propagate the uncertainty of the field observations into the...
Heceta Bank is a large reef on the edge of the central Oregon continental shelf that supports a wide variety of commercial fisheries. Using the research submersible Delta, we studied fish abundances on Heceta Bank and the relationship between species composition of fish assemblages and bottom types. Cluster analysis indicated...
Submersible belt-transect surveys along a rocky bottom were combined with acoustic surveys of the water column to estimate depth distribution and density of fishes at Stonewall Bank, Oregon in the northeastern Pacific Ocean from September through October 1991. The objectives of the study were to determine the proportion of fish...
Rockfishes, Sebastes spp.. were the most numerous and speciose fishes seen during 16 submersible dives from 64 to 305 m depth in the vicinity of Heceta Bank off the coast of Oregon. Dense schools of juvenile rockfishes and large yellowtail rockfish, S. flavidus, were observed only over rocky, high relief...
Leaf hydraulics, gas exchange and carbon storage in Pinus edulis and Juniperus monosperma, two tree species on opposite ends of the isohydry–anisohydry spectrum, were analyzed to examine relationships between hydraulic function and carbohydrate dynamics. Leaf hydraulic vulnerability, leaf water potential (Wl), leaf hydraulic conductance (Kleaf), photosynthesis (A), stomatal conductance (gs)...