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USGS2018

Wanted dead or alive: A state-space mark-recapture-recovery model incorporating multiple recovery types and state uncertainty

We developed a state-space mark-recapture-recovery model that incorporates multiple recovery types and state uncertainty to estimate survival of an anadromous fish species. We apply the model to a dataset of out-migrating juvenile steelhead trout (Oncorhynchus mykiss) tagged with passive integrated transponders, recaptured during outmigration, and recovered on bird colonies in the Columbia River basin (2008-2014). Recoveries on bird colonies are often ignored in survival studies because the river reach of mortality is often unknown, which we model as a form of state uncertainty. Median outmigration survival from release to the lower river (river kilometer 729 to 75) ranged from 0.27 to 0.35, depending on year. Recovery probabilities were frequently >0.20 in the first river reach following tagging, indicating that one out of five fish that died in that reach was recovered on a bird colony. Integrating dead recovery data provided increased parameter precision, estimation of where birds consumed fish, and survival estimates across larger spatial scales. More generally, these modeling approaches provide a flexible framework to integrate multiple sources of tag recovery data into mark-recapture studies.

Oregon, Washington↗

USGS1982

A rapid high-performance liquid-chromatographic method for simultaneously determining the concentrations of TFM and Bayer 73 in water during lampricide treatments

The high-performance liquid-chromatography (HPLC) procedure requires only minutes per sample, is specific, and is relatively sensitive (limit of detection < 0.005 mg/L for both chemicals). A combined buffer (pH 4) and internal standard (3-chlorodiphenylamine) reagent is added to the water sample, which is injected through a Sep Pak C 18 disposable cartridge. The cartridge adsorbs and retains both the lampricides and the internal standard. The quantitative elution of the three chemicals from the cartridge with a small volume of methanol effectively concentrates the sample and provides sample cleanup. The methanol extract is then analyzed directly by HPLC on an MCH 10 reverse phase column by using a methanol:0.01 mol/L acetate buffer (87:13, v:v) as the mobile phase at 2 mL/min and detected by ultraviolet spectrophotometry at 330 (or 254) nm. A microprocessor data system further facilitates the procedure by quantifying off-scale peaks and yielding results directly in units of concentration (mg/L).

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2000

Field surveys of Midwestern and Northeastern Fish and Wildlife Service lands for the presence of abnormal frogs and toads

The national distribution of information on the discovery of malformations in Minnesota frogs in 1995 stimulated collection and examination of newly metamorphosed frogs during 1996. By late summer and early fall of 1996, malformed frogs and toads were reported on U.S. Fish and Wildlife Service (USFWS) lands in Vermont (Northeast, Region 5) and Minnesota (Midwest, Region 3). In response to these reports, biologists in USFWS Regions 3 and 5 conducted a survey, during the summer of 1997 to determine the distribution and type of malformations in frogs and toads on selected federal lands. Region 3 personnel surveyed 38 field stations at National Wildlife Refuges (NWR's) and Wetland Management Districts. Malformed frogs and toads were collected at 23 (61%) of the Region 3 sites. External malformations were detected in 110 of 6632 individuals representing seven of 13 frog species and one of three toad species examined for an overall of 1.7% affected (percentages for affected species ranged from 0.4-5.2%). In Region 5, 17 NWR's and one National Park were surveyed. Malformed frogs were collected at 10 (56%) of the Region 5 sites. External malformations were detected in 58 of 2267 individuals representing six of 11 frog species and one of two toad species examined for an overall total of 2.6% affected (percentages for affected species ranged from 1.8-15.6%). The majority of malformations observed in frogs and toads collected in Regions 3 and 5 were partially or completely missing hind limbs and digits (50%)or malformed hind limbs and digits (14%). A few individuals had an extra limb or toe, missing or malformed front limb, missing eye, or malformation of the mandible. Despite small sample sizes at some sites, malformations were confirmed to be present in eight species of frogs and two species of toads on Federal lands in USFWS Regions 3 and 5. Further study is needed to determine the extent and distribution of amphibian malformations in these Regions. Data from this study were provided to the national database on distribution of malformed amphibians.

Iowa, Illinois, Michigan, Minnesnowta, Missouri, O↗

USGS2018

What can trees tell us about the air we breathe at home?

The air in houses can be affected by bad stuff, called contaminants. Sometimes harmful chemicals enter the air in buildings from nearby contaminated soil and groundwater through cracks or gaps in the foundation – a process known as vapor intrusion. This poses some risk to our health because we spend so much of our time indoors. Currently it’s difficult and expensive to figure out if vapor intrusion is happening. That’s why we wanted to see if trees can serve as indicators for vapor intrusion. We collected samples from 109 trees in a contaminated area in a Nebraska town and analyzed them for tetrachloroethene (PCE), a chemical used mostly as a cleaner and to make other chemicals. When comparing our results with the data the U.S. Environmental Protection Agency (EPA) had collected, we found that trees are good indicators of vapor intrusion.

Science Journal for Kids↗

USGS2017

Incorporating temporal heterogeneity in environmental conditions into a somatic growth model

Evaluating environmental effects on fish growth can be challenging because environmental conditions may vary at relatively fine temporal scales compared to sampling occasions. Here we develop a Bayesian state-space growth model to evaluate effects of monthly environmental data on growth of fish that are observed less frequently (e.g., from mark-recapture data where time between captures can range from months to years). We assess effects of temperature, turbidity duration, food availability, flow variability, and trout abundance on subadult humpback chub (Gila cypha) growth in two rivers, the Colorado River (CR) and the Little Colorado River (LCR), and we use out-of-sample prediction to rank competing models. Environmental covariates explained a high proportion of the variation in growth in both rivers; however, the best growth models were river-specific and included either positive temperature and turbidity duration effects (CR) or positive temperature and food availability effects (LCR). Our approach to analyzing environmental controls on growth should be applicable in other systems where environmental data vary over relatively short time scales compared to animal observations.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS1992

Functional response and capture timing in an individual-based model: predation by northern squawfish (Ptychocheilus oregonensis) on juvenile salmonids in the Columbia River

The behavior of individual northern squawfish ( Ptychocheilus oregonensis ) preying on juvenile salmonids was modeled to address questions about capture rate and the timing of prey captures (random versus contagious). Prey density, predator weight, prey weight, temperature, and diel feeding pattern were first incorporated into predation equations analogous to Holling Type 2 and Type 3 functional response models. Type 2 and Type 3 equations fit field data from the Columbia River equally well, and both models predicted predation rates on five of seven independent dates. Selecting a functional response type may be complicated by variable predation rates, analytical methods, and assumptions of the model equations. Using the Type 2 functional response, random versus contagious timing of prey capture was tested using two related models. ln the simpler model, salmon captures were assumed to be controlled by a Poisson renewal process; in the second model, several salmon captures were assumed to occur during brief "feeding bouts", modeled with a compound Poisson process. Salmon captures by individual northern squawfish were clustered through time, rather than random, based on comparison of model simulations and field data. The contagious-feeding result suggests that salmonids may be encountered as patches or schools in the river.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2000

Carbon distribution in subalpine forests and meadows of the Olympic Mountains, Washington

stimates of C storage in mountainous regions are rare. Forest–meadow ecotones in subalpine ecosystems, which contain a mosaic of forests and meadows, may be particularly sensitive to future changes in climate and are therefore important to include in estimates of terrestrial C storage. In this study, we quantified soil C and ecosystem C pools in subalpine forest and meadow soils of the northeastern (NE, dry climate) and southwestern (SW, wet climate) Olympic Mountains. Carbon concentrations of mineral soil are relatively high in upper horizons, ranging from 43 to 142 g kg −1 in NE soils and 27 to 162 g kg −1 in SW soils. Northeastern meadow soils store more C than NE forests ( P = 0.009) , while SW forest soils store more C than SW meadows ( P = 0.038) Ecosystem C storage is greater in forests than in meadows. Under a warmer climatic scenario with drier summers and wetter winters, subalpine C storage may decrease in the NE and increase in the SW, and changes in C storage will be closely related to vegetation distribution, ecosystem productivity, decomposition rates, and local disturbance regimes. Because ecosystem processes and associated C storage differ between high- and low-elevation ecosystems, it is important that data from both high- and low-elevation sites are included in estimates of C storage in terrestrial ecosystems.

Soil Science Society of America Journal↗

USGS2022

The gap between experts, farmers and non-farmers on perceived environmental vulnerability and the influence of values and beliefs

Science has played a mixed role in guiding conservation and sustainability-oriented decision-making by individuals, policymakers, institutions, and governments. Not all science-based conservation and sustainability initiatives that address issues facing humanity and ecosystems and global problems have gained public support. Conservation decisions and policy prescriptions are and may be based on perceptions about and experiences with the environment, local land use, and ecosystems that may not align with or be grounded in science or evidence from experts in the field. Values, beliefs, and perceptions associated with nature play a critical role in how individuals view biodiversity conservation, sustainability, and natural resource management . This study first examines the gap between experts (scientists and other field experts) and the public (farmers and non-farmers) about the state of water and land resources, wildlife and associated habitats, and aquatic biodiversity in the Smoky Hill River Watershed in western Kansas. Second, the study examines the role that values and beliefs play in shaping environmental perceptions for farmers and non-farmers. Analysis confirms that a gap between experts and farmers/non-farmers does exist, especially with respect to the state of the Ogallala Aquifer, playas, rivers and streams, lakes and reservoirs, native grasslands, wildlife habitats, farmland, native fish populations, and wildlife species. Ordered-logistic regression analyses, meanwhile, indicate that farmer and non-farmer perceptions about the state of the local environment are influenced by traditional and self-interested values, as well as environmental values and beliefs, but less so by religiosity and political ideology. Despite broad takeaways, results exhibited heterogeneity across the farmer and non-farmer subpopulations. If environmental professionals cannot align ecological data, stakeholders’ values/perceptions, and policies, then the existing body of technical research and management on sustainability in natural and social sciences may be of little value.

Journal of Environmental Management↗

USGS1989

Abrupt Mousterian/Aurignacian boundary at c. 40 ka bp: Accelerator 14C dates from l'Arbreda Cave (Catalunya, Spain)

The cultural transition from Mousterian to Aurignacian is abrupt at l'Arbreda Cave and occurs within a homogeneous sedimentary unit with no visible lithologic changes. Fragments of milligram-size charcoal were collected immediately above and below the cultural boundary for radiocarbon dating by accelerator. Four charcoal fragments from the lowest basal Aurignacian level yielded dates of 37·7 ± 1·0, 37·7 ± 1·0, 39·9 ± 1·2, and 38·7 ± 1·2 ka bp (average 38·5 ± 1·0 ka bp). These ages are similar to three dates from the same cultural horizon at El Castillo Cave in Cantabria and both sets of dates are significantly older than the earliest reported for the Aurignacian in the Aquitaine and in other parts of Central and Western Europe. The dates are in accord with similarly early dates for Aurignacian in Bulgaria and suggest that appearance of Aurignacian peoples is synchronous across Europe. Three fragments from the uppermost Mousterian level yielded dates of 39·4 ± 1·4, 34·1 ± 0·75, and 41·4 ± 1·6 ka bp. Discounting the spurious 34·1 ka bp result, these dates are slightly older (average 40·4 ± 1·4 ka bp) but overlap with counting error the basal Aurignacian dates. The data show that the transition from Mousterian to Aurignacian was chronologically abrupt at this location. These results strongly support the replacement hypothesis.

l'Arbreda Cave↗

USGS2023

Redd superimposition mediates the accuracy, precision, and significance of redd counts for cutthroat trout

Redd counts are commonly applied to estimate spawning population size for salmonids and allow for broad spatial and temporal coverage in monitoring efforts. However, the utility of redd counts may be compromised by observation error, particularly with respect to superimposition, where later arriving spawners construct redds overlapping existing redds. Here, we provide a mechanistic evaluation of the effects of superimposition on the error structure and biological significance of redd count data for Yellowstone cutthroat trout ( Oncorhynchus clarkii bouvieri ) spawning within tributaries to the Snake River, Wyoming. We used a Bayesian framework to parse observation error into distinct components and found low detection of redd clusters (i.e., areas of superimposition) was offset by overestimates of the number of redds per cluster, such that observed counts accurately reflected census redd abundance. However, a saturating relationship between redd counts and spawner abundance indicated that counts is best interpreted as effective reproductive effort rather than spawner abundance. Our results provide a mechanistic understanding of redd count data that can be used to assess their application and interpretation for monitoring.

Wyoming↗

USGS2001

Chemotaxonomy for naturally macerated tree-fern cuticles (Medullosales and Marattiales), Carboniferous Sydney and Mabou Sub-Basins, Nova Scotia, Canada

Naturally macerated cuticles (NMC) and one synangium, representing medullosalean and marattialean tree-fern species, from two Carboniferous coalfields in Nova Scotia, Canada, are investigated. The samples were analyzed by infrared spectroscopy (FTIR), and by pyrolysis-gas chromatograph/mass spectrometry (py-Gc/Ms) techniques in search for chemical signatures that would help in developing a chemotaxonomic classification of Carboniferous fern species, assuming genetically dependent make-up of cuticles. FTIR-derived CH2/CH3 ratios, in conjunction with contributions from carboxyl groups, demonstrated a better potential for discriminating between medullosalean genera and species than molecular signatures obtained by py-Gc/Ms. However, the latter provided better data for differentiating medullosalean from marattialean tree ferns as a group. Changes in the chemical make-up of naturally macerated cuticles due to sample preparation are discussed. ?? 2001 Elsevier Science B.V. All rights reserved.

International Journal of Coal Geology↗

USGS2016

Dynamic reusable workflows for ocean science

Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog search and data access make it now possible to create catalog-driven workflows that automate — end-to-end — data search, analysis and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill-assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enters the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic notebooks across the geoscience domains.

Journal of Marine Science and Engineering↗

USGS2001

The geology and palynology of lower and Middle Pennsylvanian strata in the Western Kentucky Coal Field

The Western Kentucky Coal Field is the southern tip of the Eastern Interior, or Illinois Basin. Pennsylvanian rocks in this area, which include conglomerate, sandstone, shale, limestone and coal, were deposited primarily in coastal-deltaic settings at a time when western Kentucky was located close to the equator. This paper discusses temporal changes in regional sedimentation patterns and coal-forming floras of Lower and Middle Pennsylvanian strata in the Western Kentucky Coal Field. Lower Pennsylvanian strata of the Caseyville Formation are characterized by paleovalley-filling sedimentation patterns and extabasinal quartz pebbles. Caseyville Formation coals are characterized thin and discontinuous and were strongly influenced by subsidence within underlying paleovalleys, and the dissected lower Pennsylvanian paleotopography. Caseyville coals are commonly dominated by Lycospora, but can also have variable palynofloras, which probably reflects variable edaphic conditions and edge effects within small, patchy paleomires. Tradewater Formation strata show increased marine influences and tidal-estuarine sedimentation, especially in the middle and upper parts. Coal beds in the lower part of the Tradewater typically are thin and discontinuous, although some economically important beds are present. Coals become thicker, more abundant and more laterally persistent towards the top of the formation. Palynologically, lower and middle Tradewater Formation coals are dominated by Lycospora, but begin to show increased amounts of tree fern spores. Middle and upper Tradewater coals are thicker and more continuous, and contain high percentages of tree fern spores. In addition, cordaite pollen is locally abundant in this interval. Carbondale and Shelburn (Desmoinesian) strata are much more laterally continuous, and occur within classic cyclothems that can be traced across the coal field. Cyclothems have long been interpreted as being eustatically driven, and glacio-eustacy controlled not only sedimentation but also the formation of Desmoinesian paleomires. Palynologically, Carbondale and Shelburn coals are either dominated by Lycospora or have heterogeneous palynofloras. Palynologic and coal-quality data suggest that hydrologic base level may have been the primary control on Desmoinesian paleomires, rather than paleoclimate, as the coals display rheotrophic, rather than ombrotrophic characteristics. ?? 2001 Elsevier Science B.V. All rights reserved.

International Journal of Coal Geology↗

USGS2023

The usability gap in water resources open data and actionable science initiatives

The open data movement represents a major advancement for informed water management. Data that are findable, accessible, interoperable, and reusable—or FAIR —are now prerequisite to responsible data stewardship. In contrast to FAIR, accessibility and usability case studies and guidelines designed around human access and understanding are lacking in the literature, especially for water resources. Such decision support guidelines are critical because (i) inherent visual design trade-offs are not best made using intuition or feedback (perceived preference), and (ii) choosing designs requires a nuanced understanding of why and how the design works (revealed effectiveness). Thus, the goal of this commentary is to highlight knowledge gaps and discuss a general usability testing method which can be applied to any water resources decision support product. The user-testing approach includes (i) interviews about visualization goals, audiences, and the uses and decisions made with the data products, (ii) diagnosis of usability challenges, and (iii) redesign of decision support products given best practices and control versus treatment with intended end-user audiences. We illustrate the method using high-profile U.S. Geological Survey water science products. In sum, optimizing and testing for usability and understandability are as central to stakeholder use as FAIR standards are, and warrant being part of the development of data products and geovisualizations.

Journal of the American Water Resources Associatio↗

USGS2018

Sampling the stream landscape: Improving the applicability of an ecoregion-level capture probability model for stream fishes

Temporal and spatial variability in streams result in heterogeneous gear capture probability (i.e., the proportion of available individuals identified) that confounds interpretation of data used to monitor fish abundance. We modeled tow-barge electrofishing capture probability at multiple spatial scales for nine Ozark Highland stream fishes. In addition to fish size, we identified seven reach-scale environmental characteristics associated with variable capture probability: stream discharge, water depth, conductivity, water clarity, emergent vegetation, wetted width–depth ratio, and proportion of riffle habitat. The magnitude of the relationship between capture probability and both discharge and depth varied among stream fishes. We also identified lithological characteristics among stream segments as a coarse-scale source of variable capture probability. The resulting capture probability model can be used to adjust catch data and derive reach-scale absolute abundance estimates across a wide range of sampling conditions with similar effort as used in more traditional fisheries surveys (i.e., catch per unit effort). Adjusting catch data based on variable capture probability improves the comparability of data sets, thus promoting both well-informed conservation and management decisions and advances in stream-fish ecology.

Arkansas, Missouri, Oklahoma↗

USGS2012

The 1170 and 1202 CE Dead Sea Rift earthquakes and long-term magnitude distribution of the Dead Sea Fault zone

In combination with the historical record, paleoseismic investigations have provided a record of large earthquakes in the Dead Sea Rift that extends back over 1500 years. Analysis of macroseismic effects can help refine magnitude estimates for large historical events. In this study we consider the detailed intensity distributions for two large events, in 1170 CE and 1202 CE, as determined from careful reinterpretation of available historical accounts, using the 1927 Jericho earthquake as a guide in their interpretation. In the absence of an intensity attenuation relationship for the Dead Sea region, we use the 1927 Jericho earthquake to develop a preliminary relationship based on a modification of the relationships developed in other regions. Using this relation, we estimate M7.6 for the 1202 earthquake and M6.6 for the 1170 earthquake. The uncertainties for both estimates are large and difficult to quantify with precision. The large uncertainties illustrate the critical need to develop a regional intensity attenuation relation. We further consider the distribution of magnitudes in the historic record and show that it is consistent with a b-value distribution with a b-value of 1. Considering the entire Dead Sea Rift zone, we show that the seismic moment release rate over the past 1500 years is sufficient, within the uncertainties of the data, to account for the plate tectonic strain rate along the plate boundary. The results reveal that an earthquake of M7.8 is expected within the zone on average every 1000 years. ?? 2011 Science From Israel/LPPLtd.

Israel Journal of Earth Sciences↗

USGS2020

Methods to quality assure, plot, summarize, interpolate, and extend groundwater-level information—Examples for the Mississippi River Valley alluvial aquifer

Large-scale computational investigations of groundwater levels are proposed to accelerate science delivery through a workflow spanning database assembly, statistics, and information synthesis and packaging. A water-availability study of the Mississippi River alluvial plain, and particularly the Mississippi River Valley alluvial aquifer (MRVA), is ongoing. Software (visGWDBmrva) has been released as part of the study that demonstrates groundwater informatics for the aquifer. Considerable water-level data collected by multiple agencies over a seven-state area exist (18,903 wells; 287,272 measurements [April 22, 2019]). Data and metadata quality assurance methods, basic statistics, hydrograph visualization, outlier identification, hypothesis testing, and time-series modeling are described. Two approaches (generalized additive models [GAMs] and support vector machines [SVMs]) are used for data interpolation and extension to monthly water-level estimates. Numerical congruence between GAM and SVM estimates will be useful to limit inclusion of monthly estimates from subsequent science activities.

Mississippi River valley↗

USGS2023

Who spawns where? Temperature, elevation, and discharge differentially affect the distribution of breeding by six Pacific salmonids within a large river basin

Within the geographic range of salmonid fishes, many apparently suitable rivers and streams are used for reproduction by some species but not others. This is widely known but seldom addressed, as studies often examine factors determining the distribution of one or only a few species. We examined physical factors associated with the spawning distribution of six native Pacific salmonids (pink, chum, coho, and Chinook salmon, bull trout, and steelhead) in the Skagit River basin, Washington. Annual mean temperature and catchment elevation had the strongest association with spawning assemblage distribution, but stream length, annual discharge, seasonal hydrology, and land use were also influential. Some species (e.g., pink and Chinook salmon) were more closely associated with each other and with common variables than others, and bull trout were the most distinctive. For interpretation, we investigated the roles of adult body size, timing of spawning, and duration of juvenile rearing, but none of these factors explained groupings in the data. Interspecific differences in habitat association remained, suggesting fundamental constraints on species distributions with implications for conservation and restoration.

Washington↗