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USGS2025

Designs for cyanobacterial harmful algal bloom monitoring in the Sacramento–San Joaquin Delta, California

Cyanobacterial harmful algal blooms (CHABs) are a growing concern in freshwater environments. These blooms can lead to degraded water quality, ecosystem disruptions, and public health threats due to the production of potent cyanotoxins. The Sacramento–San Joaquin Delta (California, USA; the Delta) has experienced CHABs since 1999, including CHABs that produce cyanotoxins at concentrations exceeding recreational advisory threshold levels. In response to the CHAB monitoring needs in the Delta, in 2024 a CHAB monitoring strategy for the Sacramento–San Joaquin Delta was released. The CHAB monitoring strategy recommended implementing a comprehensive monitoring program aligned with regional priorities, and this report responds directly to that recommendation. Building on the CHAB monitoring strategy, it describes three example monitoring designs that draw from past studies to address present needs. To develop designs, the report outlines key components and considerations for implementing a CHAB monitoring program in the Delta. It provides: background on monitoring and modeling approaches, an overview of current monitoring programs in the region, guidance for selecting monitoring locations, indicators, and sampling frequencies, and example designs to guide program planning and budgeting. The overarching goal of the report is to help agencies and stakeholders move from high-level recommendations to practical, actionable designs that are tailored to the Delta’s physical, anthropogenic, and ecological landscape.

ESS Open Archive↗

USGS2002

Beyond theories of plant invasions: Lessons from natural landscapes

There are a growing number of contrasting theories about plant invasions, but most are only weakly supported by small-scale field experiments, observational studies, and mathematical models. Among the most contentious theories is that species-rich habitats should be less vulnerable to plant invasion than species-poor sites, stemming from earlier theories that competition is a major force in structuring plant communities. Early ecologists such as Charles Darwin (1859) and Charles Elton (1958) suggested that a lack of intense interspecific competition on islands made these low-diversity habitats vulnerable to invasion. Small-scale field experiments have supported and contradicted this theory, as have various mathematical models. In contrast, many large-scale observational studies and detailed vegetation surveys in continental areas often report that species-rich areas are more heavily invaded than species-poor areas, but there are exceptions here as well. In this article, I show how these seemingly contrasting patterns converge once appropriate spatial and temporal scales are considered in complex natural environments. I suggest ways in which small-scale experiments, mathematical models, and large- scale observational studies can be improved and better integrated to advance a theoretically based understanding of plant invasions.

Comments on Theoretical Biology↗

USGS2012

Geospatial datasets for watershed delineation and characterization used in the Hawaii StreamStats web application

The U.S. Geological Survey Hawaii StreamStats application uses an integrated suite of raster and vector geospatial datasets to delineate and characterize watersheds. The geospatial datasets used to delineate and characterize watersheds on the StreamStats website, and the methods used to develop the datasets are described in this report. The datasets for Hawaii were derived primarily from 10 meter resolution National Elevation Dataset (NED) elevation models, and the National Hydrography Dataset (NHD), using a set of procedures designed to enforce the drainage pattern from the NHD into the NED, resulting in an integrated suite of elevation-derived datasets. Additional sources of data used for computing basin characteristics include precipitation, land cover, soil permeability, and elevation-derivative datasets. The report also includes links for metadata and downloads of the geospatial datasets.

Hawai'i↗

USGS2013

An anti-steroidogenic inhibitory primer pheromone in male sea lamprey (Petromyzon marinus)

Reproductive functions can be modulated by both stimulatory and inhibitory primer pheromones released by conspecifics. Many stimulatory primer pheromones have been documented, but relatively few inhibitory primer pheromones have been reported in vertebrates. The sea lamprey male sex pheromone system presents an advantageous model to explore the stimulatory and inhibitory primer pheromone functions in vertebrates since several pheromone components have been identified. We hypothesized that a candidate sex pheromone component, 7α, 12α-dihydroxy-5α-cholan-3-one-24-oic acid (3 keto-allocholic acid or 3kACA), exerts priming effects through the hypothalamic-pituitary-gonadal (HPG) axis. To test this hypothesis, we measured the peptide concentrations and gene expressions of lamprey gonadotropin releasing hormones (lGnRH) and the HPG output in immature male sea lamprey exposed to waterborne 3kACA. Exposure to waterborne 3kACA altered neuronal activation markers such as jun and jun N-terminal kinase (JNK), and lGnRH mRNA levels in the brain. Waterborne 3kACA also increased lGnRH-III, but not lGnRH-I or -II, in the forebrain. In the plasma, 3kACA exposure decreased all three lGnRH peptide concentrations after 1 h exposure. After 2 h exposure, 3kACA increased lGnRHI and -III, but decreased lGnRH-II peptide concentrations in the plasma. Plasma lGnRH peptide concentrations showed differential phasic patterns. Group housing condition appeared to increase the averaged plasma lGnRH levels in male sea lamprey compared to isolated males. Interestingly, 15α-hydroxyprogesterone (15α-P) concentrations decreased after prolonged 3kACA exposure (at least 24 h). To our knowledge, this is the only known synthetic vertebrate pheromone component that inhibits steroidogenesis in males.

General and Comparative Endocrinology↗

USGS1998

Age and growth of lake sturgeon in the Upper St. Lawrence River

The growth of lake sturgeon ( Acipenser fulvescens ) over time in the upper St. Lawrence River was examined. Growth of lake sturgeon collected during 1993 and 1994 below Robert Moses Dam near Massena, New York, was compared to that reported for the same population almost 25 years earlier. The data suggest that lake sturgeon growth was similar to that reported in the previous study. However, significant differences in the elevations of regression models between males and fish of unknown sex in both data sets suggest possible sexual dimorphism in growth at younger ages.

New York, Ontario↗

USGS2008

Complex structure within Saturn's infrared aurora

The majority of planetary aurorae are produced by electrical currents flowing between the ionosphere and the magnetosphere which accelerate energetic charged particles that hit the upper atmosphere. At Saturn, these processes collisionally excite hydrogen, causing ultraviolet emission, and ionize the hydrogen, leading to H3+ infrared emission. Although the morphology of these aurorae is affected by changes in the solar wind, the source of the currents which produce them is a matter of debate. Recent models predict only weak emission away from the main auroral oval. Here we report images that show emission both poleward and equatorward of the main oval (separated by a region of low emission). The extensive polar emission is highly variable with time, and disappears when the main oval has a spiral morphology; this suggests that although the polar emission may be associated with minor increases in the dynamic pressure from the solar wind, it is not directly linked to strong magnetospheric compressions. This aurora appears to be unique to Saturn and cannot be explained using our current understanding of Saturn's magnetosphere. The equatorward arc of emission exists only on the nightside of the planet, and arises from internal magnetospheric processes that are currently unknown. ??2008 Macmillan Publishers Limited. All rights reserved.

Nature↗

USGS2012

Mate loss affects survival but not breeding in black brant geese

For birds maintaining long-term monogamous relationships, mate loss might be expected to reduce fitness, either through reduced survival or reduced future reproductive investment. We used harvest of male brant during regular sport hunting seasons as an experimental removal to examine effects of mate loss on fitness of female black brant (Branta bernicla nigricans; hereafter brant). We used the Barker model in program MARK to examine effects of mate loss on annual survival, reporting rate, and permanent emigration. Survival rates decreased from 0.847 ± 0.004 for females who did not lose their mates to 0.690 ± 0.072 for birds who lost mates. Seber ring reporting rate for females that lost their mates were 2 times higher than those that did not lose mates, 0.12 ± 0.086 and 0.06 ± 0.006, respectively, indicating that mate loss increased vulnerability to harvest and possibly other forms of predation. We found little support for effects of mate loss on fidelity to breeding site and consequently on breeding. Our results indicate substantial fitness costs to females associated with mate loss, but that females who survived and were able to form new pair bonds may have been higher quality than the average female in the population.

Behavioral Ecology↗

USGS2019

Recognizing the Famine Early Warning Systems Network: Over 30 years of drought early warning science advances and partnerships promoting global food security

On a planet with more than 7 billion people, how do we identify the millions of drought-afflicted people who face a real threat of livelihood disruption or death without humanitarian assistance? Typically, these people are poor and heavily dependent on rainfed agriculture and livestock. Most live in Africa, Central America, or Southwest Asia. When the rains fail, incomes diminish while food prices increase, cutting off the poorest (most often women and children) from access to adequate nutrition. As seen in Ethiopia in 1984 and Somalia in 2011, food shortages can lead to famine. Yet these slow onset disasters also provide opportunities for effective intervention, as seen in Ethiopia in 2015 and Somalia in 2017. Since 1985, the US Agency for International Development's Famine Early Warning Systems Network (FEWS NET) has been providing evidence-based guidance for effective humanitarian relief efforts. FEWS NET depends on a Drought Early Warning System (DEWS) to help understand, monitor, model and predict food insecurity. Here we provide an overview of FEWS NET's DEWS using examples from recent climate extremes. While drought monitoring and prediction provides just one part of FEWS NET's monitoring system, it draws from many disciplines - remote sensing, climate prediction, agro-climatic monitoring, and hydrologic modeling. Here we describe FEWS NET's multi-agency multi-disciplinary DEWS and Food Security Outlooks. This DEWS uses diagnostic analyses to guide predictions. Mid-season droughts are monitored using multiple cutting-edge earth observing systems. Crop and hydrologic models can translate these observations into impacts. This information feeds into FEWS NET reports, helping to save lives by motivating and targeting timely humanitarian assistance.

Bulletin of the American Meteorological Society↗

USGS1999

Factors influencing counts in an annual survey of Snail Kites in Florida

Snail Kites ( Rostrhamus sociabilis ) in Florida were monitored between 1969 and 1994 using a quasi-systematic annual survey. We analyzed data from the annual Snail Kite survey using a generalized linear model where counts were regarded as overdispersed Poisson random variables. This approach allowed us to investigate covariates that might have obscured temporal patterns of population change or induced spurious patterns in count data by influencing detection rates. We selected a model that distinguished effects related to these covariates from other temporal effects, allowing us to identify patterns of population change in count data. Snail Kite counts were influenced by observer differences, site effects, effort, and water levels. Because there was no temporal overlap of the primary observers who collected count data, patterns of change could be estimated within time intervals covered by an observer, but not for the intervals among observers. Modeled population change was quite different from the change in counts, suggesting that analyses based on unadjusted counts do not accurately model Snail Kite population change. Results from this analysis were consistent with previous reports of an association between water levels and counts, although further work is needed to determine whether water levels affect actual population size as well as detection rates of Snail Kites. Although the effects of variation in detection rates can sometimes be mitigated by including controls for factors related to detection rates, it is often difficult to distinguish factors wholly related to detection rates from factors related to population size. For factors related to both, count survey data cannot be adequately analyzed without explicit estimation of detection rates, using procedures such as capture-recapture.

The Auk↗

USGS2018

Crowding affects health, growth, and behavior in headstart pens for Agassiz's desert tortoise

Worldwide, scientists have headstarted threatened and endangered reptiles to augment depleted populations. Not all efforts have been successful. For the threatened Agassiz's desert tortoise ( Gopherus agassizii ), one challenge to recovery is poor recruitment of juveniles into adult populations, and this is being addressed through headstart programs. We evaluated 8 cohorts of juvenile desert tortoises from 1 to 8 yrs old in a headstart program at Edwards Air Force Base, California, for health, behavior, and growth. We also examined capacities of the headstart pens. Of 148 juveniles evaluated for health, 99.3% were below a prime condition index; 14.9% were lethargic and unresponsive; 59.5% had protruding spinal columns and associated concave scutes; 29.1% had evidence of ant bites; and 14.2% had moderate to severe injuries to limbs or shell. Lifetime growth rates for juveniles 1–8 yrs of age were approximately two times less than growth rates reported for wild populations. Tortoises in older cohorts had higher growth rates, and models indicated that high density in pens and burrow sharing negatively affected growth rates. Densities of tortoises in pens (205–2042/ha) were 350–3500 times higher than the average density recorded in the wild (< 1/ha) for tortoises of similar sizes. The predominant forage species available to juveniles were alien annual grasses, which are nutritionally inadequate for growth. We conclude that the headstart pens were of inadequate size, likely contained too few shelters, and lacked the necessary biomass of preferred forbs to sustain the existing population. Additional factors to consider for future reptilian headstart pens include vegetative cover, food sources, soil seed banks, and soil composition.

California↗

USGS2015

Marine geophysical data collected in a shallow back-barrier estuary, Barnegat Bay, New Jersey

In 2011, the U.S. Geological Survey, in cooperation with the New Jersey Department of Environmental Protection, began a multidisciplinary research project to better understand the water quality in Barnegat Bay, New Jersey. This back-barrier estuary is experiencing degraded water quality, algal blooms, loss of seagrass, and increases in oxygen stress, macroalgae, stinging nettles, and brown tide. The spatial scale of the estuary and the scope of challenges within it necessitate a multidisciplinary approach that includes establishing the regional geology and the estuary’s physical characteristics and modeling how the estuary’s morphology interacts to affect its water quality. This report presents the data collected during this project for use in understanding the morphology and the distribution of sea-floor and sub-sea-floor sediments within Barnegat Bay, describes the methods used to collect and process those data, and includes links to the final processed datasets. These data can be used by scientists to understand the links between geomorphology, geologic framework, sediment transport, and estuarine water quality and circulation.

New Jersey↗

USGS2002

Documentation of Precipitation Runoff Modeling System modules for the Modular Modeling System modified for the Watershed and River Systems Management Program

A decision support system is being developed by the U.S. Geological Survey and the U.S. Bureau of Reclamation as part of a long-term project, the Watershed and River Systems Management Program. The goal of the program is to apply the decision support system to U.S. Bureau of Reclamation projects in the western United States. An important component of the decision support system is the physical hydrology modeling, which consists of watershed models using the U.S. Geological Survey's Precipitation-Runoff Modeling System within the Modular Modeling System. To construct models and to enhance the tools for the application of the decision support system, selected Precipitation-Runoff Modeling System modules were modified or developed. These modules are documented in this report.

Open-File Report↗

USGS2007

Rapid Method for Escherichia coli in the Cuyahoga River

This study is a continuation of a previous U.S. Geological Survey (USGS) project in cooperation with the National Park Service at Cuyahoga Valley National Park in Brecksville, Ohio. A rapid (1-hour) method for detecting Escherichia coli (E. coli) in water was tested and compared to the standard (24-hour) method for determining E. coli concentrations. Environmental data were collected to determine turbidity, rainfall, and streamflow at the time of sampling. In the previous study (2004-5), data collected were used to develop predictive models to determine recreational water quality in the river at two sites within the park. Data collected during this continued study (2006) were used to test these models. At Jaite, a centrally located site within the park, the model correctly predicted exceedances or nonexceedances of the Ohio Environmental Protection Agency maximum for recreational water quality in 80 percent of samples. At Old Portage, a site near the upstream boundary of the park, the model correctly predicted recreational water quality in 58 percent of samples. All of the data collected in 2004-6 will be used to develop more accurate models for use in future studies. Analysis and discussion of model results are scheduled to be included in an upcoming USGS Scientific Investigations Report.

Open-File Report↗

USGS2007

Phosphorus Concentrations in Stream-Water and Reference Samples - An Assessment of Laboratory Comparability

In 2003, a study was conducted to evaluate the accuracy and precision of 10 laboratories that analyze water-quality samples for phosphorus concentrations in the Catskill Mountain region of New York State. Many environmental studies in this region rely on data from these different laboratories for water-quality analyses, and the data may be used in watershed modeling and management decisions. Therefore, it is important to determine whether the data reported by these laboratories are of comparable accuracy and precision. Each laboratory was sent 12 samples for triplicate analysis for total phosphorus, total dissolved phosphorus, and soluble reactive phosphorus. Eight of these laboratories reported results that met comparability criteria for all samples; the remaining two laboratories met comparability criteria for only about half of the analyses. Neither the analytical method used nor the sample concentration ranges appeared to affect the comparability of results. The laboratories whose results were comparable gave consistently comparable results throughout the concentration range analyzed, and the differences among methods did not diminish comparability. All laboratories had high data precision as indicated by sample triplicate results. In addition, the laboratories consistently reported total phosphorus values greater than total dissolved phosphorus values, and total dissolved phosphorus values greater than soluble reactive phosphorus values, as would be expected. The results of this study emphasize the importance of regular laboratory participation in sample-exchange programs.

Open-File Report↗

USGS1995

Geochemistry of ground water in the Gallup, Dakota, and Morrison aquifers, San Juan Basin, New Mexico

Ground water was sampled from wells completed in the Gallup, Dakota, and Morrison aquifers in the San Juan Basin, New Mexico, to examine controls on solute concentrations. Samples were collected from 38 wells primarily from the Morrison aquifer (25 wells) in the northwestern part of the basin. A series of samples was collected along ground-water flow paths; dissolved constituents varied horizontally and vertically. The understanding of the flow system changed as a result of the geochemical analyses. The conceptual model of the flow system in the Morrison aquifer prior to the study reported here assumed the Westwater Canyon Member of the Morrison aquifer as the only significant regional aquifer; flow was assumed to be two dimensional; and vertical leakage was assumed to be negligible. The geochemical results indicate that the Westwater Canyon Member is not the only major water-yielding zone and that the flow system is three dimensional. The data presented in this report suggest an upward component of flow into the Morrison aquifer. The entire section above and below the Morrison aquifer appears to be controlled by a three-dimensional flow regime where saline brine leaks near the San Juan River discharge area. Predominant ions in the Gallup aquifer were calcium bicarbonate in recharge areas and sodium sulfate in discharge areas. In the Dakota aquifer, predominant ions were sodium bicarbonate and sodium sulfate. Water in the Morrison aquifer was predominantly sodium bicarbonate in the recharge area, changing to sodium sulfate downgradient. Chemical and radioisotopic data indicate that water from overlying and underlying units mixes with recharge water in the Morrison aquifer. Recharge water contained a large ratio of chlorine-36 to chlorine and a small ratio of bromide to chloride. Approximately 10 miles downgradient, samples from four wells completed in the Morrison aquifer were considerably different in composition compared to recharge samples. Oxygen stable isotopes decreased by 2.8 per mil and deuterium decreased 26 per mil, relative to recharge. Carbon-14 radioisotope activities were not detectable. Chloride-36 radioisotope ratios were small and bromide to chloride concentration ratios were large. These results suggest two potentially viable processes: ion filtration or trapping of ancient dilute water recharged under a humid climate. For water samples near the San Juan River, pH decreased to about 8.0, chloride concentrations increased to more than 100 milligrams per liter, and ratios of chlorine-36 to chlorine and bromide to chloride were small. Leakage of deep basin brine into the fresher water of the Morrison aquifer appears to control ion concentrations.

Water-Resources Investigations Report↗

USGS2024

Population and spatial dynamics of desert bighorn sheep in Grand Canyon during an outbreak of respiratory pneumonia

Introduction: Terrestrial species in riverine ecosystems face unique constraints leading to diverging patterns of population structure, connectivity, and disease dynamics. Desert bighorn sheep ( Ovis canadensis nelsoni ) in Grand Canyon National Park, a large native population in the southwestern USA, offer a unique opportunity to evaluate population patterns and processes in a remote riverine system with ongoing anthropogenic impacts. We integrated non-invasive, invasive, and citizen-science methods to address questions on abundance, distribution, disease status, genetic structure, and habitat fragmentation. Methods: We compiled bighorn sightings collected during river trips by park staff, commercial guides, and private citizens from 2000–2018 and captured bighorn in 2010–2016 to deploy GPS collars and test for disease. From 2011–2015, we non-invasively collected fecal samples and genotyped them at 9–16 microsatellite loci for individual identification and genetic structure. We used assignment tests to evaluate genetic structure and identify subpopulations, then estimated gene flow and recent migration to evaluate fragmentation. We used spatial capture-recapture to estimate annual population size, distribution, and trends after accounting for spatial variation in detection with a resource selection function model. Results and discussion: From 2010–2018, 3,176 sightings of bighorn were reported, with sightings of 56–145 bighorn annually on formal surveys. From 2012–2016, bighorn exhibiting signs of respiratory disease were observed along the river throughout the park. Of 25 captured individuals, 56% were infected by Mycoplasma ovipneumoniae , a key respiratory pathogen, and 81% were recently exposed. Pellet sampling for population estimation from 2011–2015 yielded 1,250 genotypes and 453 individuals. We detected 6 genetic clusters that exhibited mild to moderate genetic structure ( F ST 0.022–0.126). The river, distance, and likely topography restricted recent gene flow, but we detected cross-river movements in one section via genetic recaptures, no subpopulation appeared completely isolated, and genetic diversity was among the highest reported. Recolonization of one large stretch of currently empty habitat appears limited by the constrained topology of this system. Annual population estimates ranged 536–552 (95% CrI range 451–647), lamb:ewe ratios varied, and no significant population decline was detected. We provide a multi-method sampling framework useful for sampling other wildlife in remote riverine systems.

Arizona↗

USGS2016

Abiotic raw-materials in life cycle impact assessments: An emerging consensus across disciplines

This paper captures some of the emerging consensus points that came out of the workshop “Mineral Resources in Life Cycle Impact Assessment: Mapping the path forward”, held at the Natural History Museum London on 14 October 2015: that current practices rely in many instances on obsolete data, often confuse resource depletion with impacts on resource availability, which can therefore provide inconsistent decision support and lead to misguided claims about environmental performance. Participants agreed it would be helpful to clarify which models estimate depletion and which estimate availability, so that results can be correctly reported in the most appropriate framework. Most participants suggested that resource availability will be more meaningfully addressed within a comprehensive Life Cycle Sustainability Assessment framework rather than limited to an environmental Life Cycle Assessment or Footprint. Presentations from each of the authors are available for download.

Resources↗

USGS1978

Definition of regional relationships between dissolved solids and specific conductance, Susquehanna River basin, Pennsylvania and New York

This report presents statistical tests for assessing the accuracy and validity of two regional models of the relationship between dissolved-solids concentration and specific conductance. These models are used to estimate dissolved-solids concentrations based on specific-conductance measurements. The two regional models are compared with station models for 27 stream sites in the Susquehanna River basin. The average standard errors of estimate of two regional models, when used to estimate dissolved-solids concentrations for the 27 stream sites, are 10.7 and 10.6 percent. In comparison, the station models have average standard errors of 9.0 and 9.3 percent, respectively. Results of the statistical tests indicate that in the Susquehanna River basin the regional models can be used to estimate dissolved-solids concentrations from specific-conductance data for sites for which chemical analyses are not available.

New York, Pennsylvania↗