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USGS2023

Aging contrast: A contrastive learning framework for fish re-identification across seasons and years.

The fields of biology, ecology, and fisheries management are witnessing a growing demand for distinguishing individual fish. In recent years, deep learning methods have emerged as a promising tool for image-based fish recognition. Our study is focused on the re-identification of masu salmon from Japan, wherein fish were individually marked and photographed to evaluate discriminative body characteristics. Unlike previous studies where fish were sampled during the same time period, we evaluated individual re-identification across seasons and years to address challenges due to aging, seasonal variation, and other factors. In this paper, we propose a new contrastive learning framework called Ag ing Co ntrast (AgCo) and evaluate its performance on the masu salmon dataset. Our analysis indicates that, unlike large changes in body size over time, the pattern of parr marks on the lateral line of the fish body remains relatively stable, despite some change in coloration across seasons. AgCo accounts for such seasonally-invariant features and performs re-identification based on the cosine similarity of these features. Extensive experiments show that our AgCo method outperforms other state-of-the-art methods.

Conference Paper↗

USGS2011

Degradation of the disease-associated prion protein by a serine protease from lichens

The disease-associated prion protein (PrP(TSE)), the probable etiological agent of the transmissible spongiform encephalopathies (TSEs), is resistant to degradation and can persist in the environment. Lichens, mutualistic symbioses containing fungi, algae, bacteria and occasionally cyanobacteria, are ubiquitous in the environment and have evolved unique biological activities allowing their survival in challenging ecological niches. We investigated PrP(TSE) inactivation by lichens and found acetone extracts of three lichen species (Parmelia sulcata, Cladonia rangiferina and Lobaria pulmonaria) have the ability to degrade prion protein (PrP) from TSE-infected hamsters, mice and deer. Immunoblots measuring PrP levels and protein misfolding cyclic amplification indicated at least two logs of reductions in PrP(TSE). Degradative activity was not found in closely related lichen species or in algae or a cyanobacterium that inhabit lichens. Degradation was blocked by Pefabloc SC, a serine protease inhibitor, but not inhibitors of other proteases or enzymes. Additionally, we found that PrP levels in PrP(TSE)-enriched preps or infected brain homogenates are also reduced following exposure to freshly-collected P. sulcata or an aqueous extract of the lichen. Our findings indicate that these lichen extracts efficiently degrade PrP(TSE) and suggest that some lichens could have potential to inactivate TSE infectivity on the landscape or be a source for agents to degrade prions. Further work to clone and characterize the protease, assess its effect on TSE infectivity and determine which organism or organisms present in lichens produce or influence the protease activity is warranted.

PLoS ONE↗

USGS1975

Studies on combined effects of organophosphates and heavy metals in birds. I. Plasma and brain cholinesterase in Coturnix quail fed methyl mercury and orally dosed with parathion

We found that mercury potentiated the toxicity and biochemical effects of parathion. Male Coturnix quail (Coturnix coturnix japonica) were fed a sublethal concentration of morsodren (4 ppm as methyl mercury) for 18 weeks. This resulted in an accumulation of 21.0 ppm of mercury in the liver and 8.4 ppm in the carcass. Birds fed clean feed and those fed morsodren-treated feed were orally dosed with 2, 4, 6, 8,and 10 mg/kg parathion, and their 48-h survival times compared. The computed LD50 was 5.86mg/kg in birds not fed morsodren and 4.24 in those fed the heavy metal. When challenged with a sublethal, oral dose of parathion (1.0 mg/kg), morsodren-fed birds exhibited significantly greater inhibition of plasma and brain cholinesterase activity than controls dosed with parathion. Brain cholinesterase activity was inhibited 41% in morsodren-fed birds and 26in clean-fed birds dosed with parathion, which suggested that the increase in parathion toxicity in the presence of morsodren was directly related to the inhibitation of brain cholinesterase.

Bulletin of Environmental Contamination and Toxico↗

USGS2006

The effect of multiple stressors on salt marsh end-of-season biomass

It is becoming more apparent that commonly used statistical methods (e.g. analysis of variance and regression) are not the best methods for estimating limiting relationships or stressor effects. A major challenge of estimating the effects associated with a measured subset of limiting factors is to account for the effects of unmeasured factors in an ecologically realistic matter. We used quantile regression to elucidate multiple stressor effects on end-of-season biomass data from two salt marsh sites in coastal Louisiana collected for 18 yr. Stressor effects evaluated based on available data were flooding, salinity air temperature, cloud cover, precipitation deficit, grazing by muskrat, and surface water nitrogen and phosphorus. Precipitation deficit combined with surface water nitrogen provided the best two-parameter model to explain variation in the peak biomass with different slopes and intercepts for the two study sites. Precipitation deficit, cloud cover, and temperature were significantly correlated with each other. Surface water nitrogen was significantly correlated with surface water phosphorus and muskrat density. The site with the larger duration of flooding showed reduced peak biomass, when cloud cover and surface water nitrogen were optimal. Variation in the relatively low salinity occurring in our study area did not explain any of the variation in Spartina alterniflora biomass.

Estuaries and Coasts↗

USGS1999

Techniques for restoration of disturbed coastal wetlands of the Great Lakes

A long history of human-induced degradation of Great Lakes wetlands has made restoration a necessity, but the practice of wetland restoration is relatively new, especially in large lake systems. Therefore, we compiled tested methods and developed additional potential methods based on scientific understanding of Great Lakes wetland ecosytems to providc an overview of approaches for restoration. We addressed this challenge by focusing on four general fields of science: hydrology, sedimentology, chemistry, and biology. Hydrologic remediation methods include restoring hydrologic connections between diked and hydrologically altered wetlands and the lakes, restoring water tables lowered by ditching, and restoring natural variation in lake levels of regulated lakes Superior and Ontario. Sedimentological remediation methods include management of sediment input from uplands, removal or proper management of dams on tributary rivers, and restoration of protective barrier beaches and sand spits. Chemical remediation methods include reducing or eliminating inputs of contaminants from point and non-pont sources, natural sediment remediation by biodegradation and chemical degradation, and active sediment remediation by removal or by in situ treatment Biological remediation methods include control of non-target organisms, enhancing populations of target organisms, and enhancing habitat for target organisms. Some of these method were used in three major restoration projects (Metzger Marsh on Lake Erie and Cootes Paradise and Oshawa Second Marsh on Lake Ontario), which are described as case studies to show practical applications of wetland restoration in the Great Lakes. Successful restoration techniques that do not require continued manipulation must be founded in the basic tenets of ecology and should mimic natural processes. Success is demonstrated by the sustainability, productivity, nutrient-retention ability, invasibility, and biotic interactions within a restored wetland.

Wetlands↗

USGS2003

Volcano seismology

A fundamental goal of volcano seismology is to understand active magmatic systems, to characterize the configuration of such systems, and to determine the extent and evolution of source regions of magmatic energy. Such understanding is critical to our assessment of eruptive behavior and its hazardous impacts. With the emergence of portable broadband seismic instrumentation, availability of digital networks with wide dynamic range, and development of new powerful analysis techniques, rapid progress is being made toward a synthesis of high-quality seismic data to develop a coherent model of eruption mechanics. Examples of recent advances are: (1) high-resolution tomography to image subsurface volcanic structures at scales of a few hundred meters; (2) use of small-aperture seismic antennas to map the spatio-temporal properties of long-period (LP) seismicity; (3) moment tensor inversions of very-long-period (VLP) data to derive the source geometry and mass-transport budget of magmatic fluids; (4) spectral analyses of LP events to determine the acoustic properties of magmatic and associated hydrothermal fluids; and (5) experimental modeling of the source dynamics of volcanic tremor. These promising advances provide new insights into the mechanical properties of volcanic fluids and subvolcanic mass-transport dynamics. As new seismic methods refine our understanding of seismic sources, and geochemical methods better constrain mass balance and magma behavior, we face new challenges in elucidating the physico-chemical processes that cause volcanic unrest and its seismic and gas-discharge manifestations. Much work remains to be done toward a synthesis of seismological, geochemical, and petrological observations into an integrated model of volcanic behavior. Future important goals must include: (1) interpreting the key types of magma movement, degassing and boiling events that produce characteristic seismic phenomena; (2) characterizing multiphase fluids in subvolcanic regimes and determining their physical and chemical properties; and (3) quantitatively understanding multiphase fluid flow behavior under dynamic volcanic conditions. To realize these goals, not only must we learn how to translate seismic observations into quantitative information about fluid dynamics, but we also must determine the underlying physics that governs vesiculation, fragmentation, and the collapse of bubble-rich suspensions to form separate melt and vapor. Refined understanding of such processes—essential for quantitative short-term eruption forecasts—will require multidisciplinary research involving detailed field measurements, laboratory experiments, and numerical modeling.

Pure and Applied Geophysics↗

USGS2008

Interactive visualization to advance earthquake simulation

The geological sciences are challenged to manage and interpret increasing volumes of data as observations and simulations increase in size and complexity. For example, simulations of earthquake-related processes typically generate complex, time-varying data sets in two or more dimensions. To facilitate interpretation and analysis of these data sets, evaluate the underlying models, and to drive future calculations, we have developed methods of interactive visualization with a special focus on using immersive virtual reality (VR) environments to interact with models of Earth's surface and interior. Virtual mapping tools allow virtual "field studies" in inaccessible regions. Interactive tools allow us to manipulate shapes in order to construct models of geological features for geodynamic models, while feature extraction tools support quantitative measurement of structures that emerge from numerical simulation or field observations, thereby enabling us to improve our interpretation of the dynamical processes that drive earthquakes. VR has traditionally been used primarily as a presentation tool, albeit with active navigation through data. Reaping the full intellectual benefits of immersive VR as a tool for scientific analysis requires building on the method's strengths, that is, using both 3D perception and interaction with observed or simulated data. This approach also takes advantage of the specialized skills of geological scientists who are trained to interpret, the often limited, geological and geophysical data available from field observations. ?? Birkhaueser 2008.

Pure and Applied Geophysics↗

USGS2017

Longitudinal thermal heterogeneity in rivers and refugia for coldwater species: Effects of scale and climate change

Climate-change driven increases in water temperature pose challenges for aquatic organisms. Predictions of impacts typically do not account for fine-grained spatiotemporal thermal patterns in rivers. Patches of cooler water could serve as refuges for anadromous species like salmon that migrate during summer. We used high-resolution remotely sensed water temperature data to characterize summer thermal heterogeneity patterns for 11,308 km of second–seventh-order rivers throughout the Pacific Northwest and northern California (USA). We evaluated (1) water temperature patterns at different spatial resolutions, (2) the frequency, size, and spacing of cool thermal patches suitable for Pacific salmon (i.e., contiguous stretches ≥ 0.25 km, ≤ 15 °C and ≥ 2 °C, aooler than adjacent water), and (3) potential influences of climate change on availability of cool patches. Thermal heterogeneity was nonlinearly related to the spatial resolution of water temperature data, and heterogeneity at fine resolution (< 1 km) would have been difficult to quantify without spatially continuous data. Cool patches were generally > 2.7 and < 13.0 km long, and spacing among patches was generally > 5.7 and < 49.4 km. Thermal heterogeneity varied among rivers, some of which had long uninterrupted stretches of warm water ≥ 20 °C, and others had many smaller cool patches. Our models predicted little change in future thermal heterogeneity among rivers, but within-river patterns sometimes changed markedly compared to contemporary patterns. These results can inform long-term monitoring programs as well as near-term climate-adaptation strategies.

California, Idaho, Oregon, Washington↗

USGS2015

Measurement of slow-moving along-track displacement from an efficient multiple-aperture SAR interferometry (MAI) stacking

Multiple-aperture SAR interferometry (MAI) has demonstrated outstanding measurement accuracy of along-track displacement when compared to pixel-offset-tracking methods; however, measuring slow-moving (cm/year) surface displacement remains a challenge. Stacking of multi-temporal observations is a potential approach to reducing noise and increasing measurement accuracy, but it is difficult to achieve a significant improvement by applying traditional stacking methods to multi-temporal MAI interferograms. This paper proposes an efficient MAI stacking method, where multi-temporal forward- and backward-looking residual interferograms are individually stacked before the MAI interferogram is generated. We tested the performance of this method using ENVISAT data from Kīlauea Volcano, Hawai‘i, where displacement on the order of several centimeters per year is common. By comparing results from the proposed stacking methods with displacements from GPS data, we documented measurement accuracies of about 1.03 and 1.07 cm/year for the descending and ascending tracks, respectively—an improvement of about a factor of two when compared with that from the conventional stacking approach. Three-dimensional surface-displacement maps can be constructed by combining stacked InSAR and MAI observations, which will contribute to a better understanding of a variety of geological phenomena.

Hawaii↗

USGS1997

Resolution of matrix effects on analysis of total and methyl mercury in aqueous samples from the Florida Everglades

Aqueous samples from the Florida Everglades present several problems for the analysis of total mercury (HgT) and methyl mercury (MeHg). Constituents such as dissolved organic carbon (DOC) and sulfide at selected sites present particular challenges due to interferences with standard analytical techniques. This is manifested by 1) the inability to discern when bromine monochloride (BrCl) addition is sufficient for sample oxidation for HgT analysis; and 2) incomplete spike recoveries using the distillation/ethylation technique for MeHg analysis. Here, we suggest ultra-violet (UV) oxidation prior to addition of BrCl to ensure total oxidation of DOC prior to HgT analysis and copper sulfate (CuSO 4 ) addition to aid in distillation in the presence of sulfide for MeHg analysis. Despite high chloride (Cl - ) levels, we observed no effects on MeHg distillation/ethylation analyses.

Fresenius' Journal of Analytical Chemistry↗

USGS2014

Estimates of vital rates for a declining loggerhead turtle ( Caretta caretta ) subpopulation: implications for management

Because subpopulations can differ geographically, genetically and/or phenotypically, using data from one subpopulation to derive vital rates for another, while often unavoidable, is not optimal. We used a two-state open robust design model to analyze a 14-year dataset (1998–2011) from the St. Joseph Peninsula, Florida (USA; 29.748°, −85.400°) which is the densest loggerhead (Caretta caretta) nesting beach in the Northern Gulf of Mexico subpopulation. For these analyses, 433 individuals were marked of which only 7.2 % were observed re-nesting in the study area in subsequent years during the study period. Survival was estimated at 0.86 and is among the highest estimates for all subpopulations in the Northwest Atlantic population. The robust model estimated a nesting assemblage size that ranged from 32 to 230 individuals each year with an annual average of 110. The model estimates indicated an overall population decline of 17 %. The results presented here for this nesting group represent the first estimates for this subpopulation. These data provide managers with information specific to this subpopulation that can be used to develop recovery plans and conduct subpopulation-specific modeling exercises explicit to the challenges faced by turtles nesting in this region.

Florida↗

USGS2022

Chloride toxicity to native freshwater species in natural and reconstituted prairie pothole waters

Oil and gas extraction in the Prairie Pothole Region (PPR) of the northern USA has resulted in elevated chloride concentrations in ground and surface water due to widespread contamination with highly saline produced water, or brine. The toxicity of chloride is poorly understood in the high hardness waters characteristic of the region. We evaluated the toxicity of chloride to two endemic species, Daphnia magna (water flea) and Lemna gibba (duckweed), exposed in field-collected waters (hardness ~ 3000 mg/L as CaCO 3 ) and reconstituted waters (hardness 370 mg/L as CaCO 3 ) intended to mimic PPR background waters. We also investigated the role of chloride in the toxicity of water reconstituted to mimic legacy brine-contaminated wetlands, using two populations of native Pseudacris maculata (Boreal Chorus Frog). Chloride toxicity was similar in field-collected and reconstituted waters for both D. magna (LC50s 3070–3788 mg Cl −1 /L) and L. gibba (IC50s 2441–2887). Although hardness can ameliorate chloride toxicity at low to high hardness, we did not observe additional protection as hardness increased from 370 to ~ 3000 mg/L. In P. maculata exposures, chloride did not fully explain toxicity. Chloride sensitivity also differed between populations, with mortality at 2000 mg Cl − /L in one population but not the other, and population-specific growth responses. Overall, these results (1) document toxicity to native species at chloride concentrations occurring in the PPR, (2) indicate that very high hardness in the region’s waters may not provide additional protection against chloride and (3) highlight challenges of brine investigations, including whether surrogate study populations are representative of local populations.

Missouri, Montana, North Dakota, Wyoming↗

USGS2012

Sea lamprey orient toward a source of a synthesized pheromone using odor-conditioned rheotaxis

Characterization of vertebrate chemo-orientation strategies over long distances is difficult because it is often not feasible to conduct highly controlled hypothesis-based experiments in natural environments. To overcome the challenge, we couple in-stream behavioral observations of female sea lampreys ( Petromyzon marinus ) orienting to plumes of a synthesized mating pheromone, 7a,12a,24-trihydroxy-5a-cholan-3-one-24-sulfate (3kPZS), and engineering algorithms to systematically test chemo-orientation hypotheses. In-stream field observations and simulated movements of female sea lampreys according to control algorithms support that odor-conditioned rheotaxis is a component of the mechanism used to track plumes of 3kPZS over hundreds of meters in flowing water. Simulated movements of female sea lampreys do not support that rheotaxis or klinotaxis alone is sufficient to enable the movement patterns displayed by females in locating 3kPZS sources in the experimental stream. Odor-conditioned rheotaxis may not only be effective at small spatial scales as previous described in crustaceans, but may also be effectively used by fishes over hundreds of meters. These results may prove useful for developing management strategies for the control of invasive species that exploit the odor-conditioned tracking behavior and for developing biologically inspired navigation strategies for robotic fish.

Behavioral Ecology and Sociobiology↗

USGS2022

Offspring sex ratios are male-biased reflecting sex-biased dispersal in Idaho, USA, wolves.

Offspring sex ratios can vary widely across species, and the reasons for such variation have long intrigued ecologists. For group-living animals, predicting offspring sex ratios as a function of group and environmental characteristics can be challenging. Additionally, mortality of group members can upend traditional theory used to explain offspring sex ratios observed in populations. Gray wolves ( Canis lupus ) in Idaho, USA, are an excellent study species for asking questions about offspring sex ratios given their group-living behavior and persistent exposure to human-caused mortality. I hypothesized that offspring sex ratios would be influenced by the characteristics of individuals, groups, and populations. I generated genotypes for 419 adult and 400 pup wolves during 2008–2018. There was a significant male-bias in litters of wolf pups with nearly 12% more male pups born than females. The individual, group, and population variables I considered did not have significant associations with offspring sex ratios. Local resource competition helped explain offspring sex ratios in wolves in my study system, but not local resource enhancement theory. Although female helpers have been shown to help slightly more than males, offspring sex ratios did not favor the helping sex suggesting that the overall benefit of female helpers may have been negligible in wolf groups during my study. Three wolf groups consistently overproduced males, the dispersing sex, suggesting that habitat quality was poor in their territories. The male-biased offspring sex ratios observed throughout this population reflect sex-biased dispersal in wolves in Idaho. Such a pattern suggests breeding females may be reducing local resource competition (e.g., mates and successful reproduction) by producing more males than females.

Idaho↗

USGS2003

Sustainable Land Use Requires Attention to Ecological Signals

This case study details the difficulties of landscape management, highlighting the challenges inherent in managing natural resources when multiple agencies are involved, when the land users have no incentive for conservation, and when government agencies have too few resources for effective management. Pumping of groundwater from the aquifer of La Costa de Hermosillo in the state of Sonora, Mexico, began in 1945 and developed so quickly that by the late 1950s salinity intrusion from the Gulf of California was occurring in the wells. In the 1970s, the irrigatable land in La Costa peaked at 132,516 ha and the extracted volume of water from the aquifer peaked at around 1.14 billion cubic meters annually. By the 1980s, 105 wells of the total of 498 were contaminated with seawater and, therefore, identified for closure. At present La Costa de Hermosillo still represents 15% of the total harvested land, 16% of the total annual production, and 23% of the gross agricultural production of the state of Sonora. However, there are approximately 80,000 ha of abandoned fields due to salt water intension, lack of water and/or lack of credit available to individual farmers. This unstable situation resulted from the interplay of water management policies and practices, and farm-land policies and practices. While government agencies have been able to enforce better water use for agricultural production, there remains a significant area that requires restoration from its degraded state. For this piece of the ecosystem management puzzle, government agencies have thus far been unable to affect a solution.

Environmental Management↗

USGS2004

Ecoregions and ecoregionalization: geographical and ecological perspectives

Ecoregions, i.e., areas exhibiting relative homogeneity of ecosystems, are units of analysis that are increasingly important in environmental assessment and management. Ecoregions provide a holistic framework for flexible, comparative analysis of complex environmental problems. Ecoregions mapping has intellectual foundations in both geography and ecology. However, a hallmark of ecoregions mapping is that it is a truly interdisciplinary endeavor that demands the integration of knowledge from a multitude of sciences. Geographers emphasize the role of place, scale, and both natural and social elements when delineating and characterizing regions. Ecologists tend to focus on environmental processes with special attention given to energy flows and nutrient cycling. Integration of disparate knowledge from the many key sciences has been one of the great challenges of ecoregions mapping, and may lie at the heart of the lack of consensus on the “optimal” approach and methods to use in such work. Through a review of the principal existing US ecoregion maps, issues that should be addressed in order to advance the state of the art are identified. Research related to needs, methods, data sources, data delivery, and validation is needed. It is also important that the academic system foster education so that there is an infusion of new expertise in ecoregion mapping and use.

Environmental Management↗

USGS2004

Contemporary carbon dynamics in terrestrial ecosystems in the Southeastern Plains of the United States

Quantifying carbon dynamics over large areas is frequently hindered by the lack of consistent, high-quality, spatially explicit land use and land cover change databases and appropriate modeling techniques. In this paper, we present a generic approach to address some of these challenges. Land cover change information in the Southeastern Plains ecoregion was derived from Landsat data acquired in 1973, 1980, 1986, 1992, and 2000 within 11 randomly located 20-km × 20-km sample blocks. Carbon dynamics within each of the sample blocks was simulated using the General Ensemble Biogeochemical Modeling System (GEMS), capable of assimilating the variances and covariance of major input variables into simulations using an ensemble approach. Results indicate that urban and forest areas have been increasing, whereas agricultural land has been decreasing since 1973. Forest clear-cutting activity has intensified, more than doubling from 1973 to 2000. The Southeastern Plains has been acting as a carbon sink since 1973, with an average rate of 0.89 Mg C/ha/yr. Biomass, soil organic carbon (SOC), and harvested materials account for 56%, 34%, and 10% of the sink, respectively. However, the sink has declined continuously during the same period owing to forest aging in the northern part of the ecoregion and increased forest clear-cutting activities in the south. The relative contributions to the sink from SOC and harvested materials have increased, implying that these components deserve more study in the future. The methods developed here can be used to quantify the impacts of human management activities on the carbon cycle at landscape to global scales.

Environmental Management↗

USGS2010

An integrated sampling and analysis approach for improved biodiversity monitoring

Successful biodiversity conservation requires high quality monitoring data and analyses to ensure scientifically defensible policy, legislation, and management. Although monitoring is a critical component in assessing population status and trends, many governmental and non-governmental organizations struggle to develop and implement effective sampling protocols and statistical analyses because of the magnitude and diversity of species in conservation concern. In this article we describe a practical and sophisticated data collection and analysis framework for developing a comprehensive wildlife monitoring program that includes multi-species inventory techniques and community-level hierarchical modeling. Compared to monitoring many species individually, the multi-species approach allows for improved estimates of individual species occurrences, including rare species, and an increased understanding of the aggregated response of a community to landscape and habitat heterogeneity. We demonstrate the benefits and practicality of this approach to address challenges associated with monitoring in the context of US state agencies that are legislatively required to monitor and protect species in greatest conservation need. We believe this approach will be useful to regional, national, and international organizations interested in assessing the status of both common and rare species.

Environmental Management↗