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At least 1,513 records · Page 84Linked to original sources
USGS2002

Threats to desert tortoise populations: a critical review of the literature

Decision in resource management are generally based on a combination of sociopolitical, economic, and environmental factors, and may be biased by personal values. These three components often contradict each other resulting in controversy. Controversies can usually be reduced when solid scientific evidence is used to support or refute a decision. However, it is important to recognize that data often do little to alter antagonists' positions when differences in values are the bases if the dispute. But, supporting data can make the decision more defensible, both legally and ethically, especially if the data supporting all opposing viewpoints are included in the decision-making process. Resource management decisions must be made using the best scientific information currently available. However, scientific data vary in two important measures of quality: reliability and validity. The reliability of the data is a measure of the degree to which the observations or conclusion can be repeated. Validity of the data is a measure of the degree to which the observation or conclusion reflects what actually occurs in nature. How the data are collected strongly affects the reliability of validity of ecological conclusions that can be made. Research data potentially relevant to management come from different sources, and the source often provides clues to the reliability and, to a certain extent, validity of data. Understanding the quality of data being used to make management decisions helps to separate the philosophical or value-based aspects of arguments from the objective ones, thus helping to clarify the decisions and judgments that need to be made. The West Mojave Plan is a multispecies, bioregional plan for the management of natural resources within a 9.4 million-acre area of the Mojave Desert in California. The plan addresses the legal requirements for the recovery of the desert tortoise ( Gopherus agazzizii ), a threatened species, but also covers an additional approximately 80 species of plants and animals assigned special status by the Bureau of Land Management, U. S. Fish and Wildlife Service, and California Department of Fish and Game. Within the planning area, 28 separate jurisdictions (counties, cities, towns, military installations, etc.) seek programmatic prescriptions that will facilitate streamlined environmental review, result in expedited authorization for development projects, and protect listed and unlisted species into the foreseeable future to avoid or minimize conflicts between proposed development and species' conservation and recovery. All of the scientific data available concerning the biology and management of these approximately 80 species and their habitats must be evaluated to develop a scientifically credible plan. This document provides an overview and evaluation of the knowledge of the major threats to the persistence and recovery of desert tortoise populations. I was specifically asked to evaluate the scientific veracity of the data and reports available. I summarize the data presently available with particular focus on the West Mojave Desert, evaluate the scientific integrity of the data. and identify major gaps in the available knowledge. I do not attempt to provide in-depth details on each study or threat; for more details I encourage the reader to consult the individual papers or reports city throughout this report (many of which are available at most university libraries and at the West Mojave Plan office in Riverside, California). I also do not attempt to characterize or evaluate the past or present management actions, except where they have direct bearing on evaluation of threats, nor do I attempt, for the most part, to acquire, generate, or evaluate new or existing, but uninterpreted data.

California↗
USGS2025

Relative abundance, seasonal occurrence, and distribution of marine birds in the northern Gulf of Mexico

Marine birds in the U.S. Gulf of Mexico have long been poorly studied. Given statutory obligations to protect migratory birds and endangered species, three broad-scale vessel and aerial programs initiated since 2010 have now surveyed the entire northern Gulf. Vessel coverage alone exceeds 700 d and 74,000 km of observer effort using 300-m strip transects. We supplemented these survey data with earlier, smaller-scale studies, eBird checklists, literature reviews, and other less accessible sources to create snapshot summaries of relative abundance, seasonal occurrence, and regional distribution for 117 taxa of marine and water birds reported from the northern Gulf (113 of which were substantiated with physical evidence). Using taxonomic and functional criteria, we identified 56 taxa characteristic of open shelf, slope, and pelagic waters (federal jurisdiction), 41 taxa with primarily coastal affinities (state and federal jurisdiction), and 20 taxa of sea and diving ducks. High species richness of marine birds in the northern Gulf is attributed to (1) a temperate-to-tropical gradient facilitating diverse marine environments year-round; (2) varied geographic origins of marine bird species using the Gulf; and (3) a mostly enclosed sea basin acting as a vagrant trap for wide-ranging species. Our taxonomic list and status updates seek to bridge information gaps for marine birds now subject to accelerated commercial uses of this region's continental shelf, including newly proposed offshore wind energy development. Other applications include guiding risk and vulnerability assessments of Gulf marine birds, providing core content for seabird observer training, and prioritizing environmental impact reviews and monitoring programs in offshore energy construction and operations plans.

Marine Ornithology: Journal of Seabird Research an↗
USGS2012

Moderate-resolution sea surface temperature data and seasonal pattern analysis for the Arctic Ocean ecoregions

Sea surface temperature (SST) is an important environmental characteristic in determining the suitability and sustainability of habitats for marine organisms. In particular, the fate of the Arctic Ocean, which provides critical habitat to commercially important fish, is in question. This poses an intriguing problem for future research of Arctic environments - one that will require examination of long-term SST records. This publication describes and provides access to an easy-to-use Arctic SST dataset for ecologists, biogeographers, oceanographers, and other scientists conducting research on habitats and/or processes in the Arctic Ocean. The data cover the Arctic ecoregions as defined by the "Marine Ecoregions of the World" (MEOW) biogeographic schema developed by The Nature Conservancy as well as the region to the north from approximately 46°N to about 88°N (constrained by the season and data coverage). The data span a 29-year period from September 1981 to December 2009. These SST data were derived from Advanced Very High Resolution Radiometer (AVHRR) instrument measurements that had been compiled into monthly means at 4-kilometer grid cell spatial resolution. The processed data files are available in ArcGIS geospatial datasets (raster and point shapefiles) and also are provided in text (.csv) format. All data except the raster files include attributes identifying latitude/longitude coordinates, and realm, province, and ecoregion as defined by the MEOW classification schema. A seasonal analysis of these Arctic ecoregions reveals a wide range of SSTs experienced throughout the Arctic, both over the course of an annual cycle and within each month of that cycle. Sea ice distribution plays a major role in SST regulation in all Arctic ecoregions.

Open-File Report↗
USGS2002

Beowulf Distributed Processing and the United States Geological Survey

Introduction In recent years, the United States Geological Survey's (USGS) National Mapping Discipline (NMD) has expanded its scientific and research activities. Work is being conducted in areas such as emergency response research, scientific visualization, urban prediction, and other simulation activities. Custom-produced digital data have become essential for these types of activities. High-resolution, remotely sensed datasets are also seeing increased use. Unfortunately, the NMD is also finding that it lacks the resources required to perform some of these activities. Many of these projects require large amounts of computer processing resources. Complex urban-prediction simulations, for example, involve large amounts of processor-intensive calculations on large amounts of input data. This project was undertaken to learn and understand the concepts of distributed processing. Experience was needed in developing these types of applications. The idea was that this type of technology could significantly aid the needs of the NMD scientific and research programs. Porting a numerically intensive application currently being used by an NMD science program to run in a distributed fashion would demonstrate the usefulness of this technology. There are several benefits that this type of technology can bring to the USGS's research programs. Projects can be performed that were previously impossible due to a lack of computing resources. Other projects can be performed on a larger scale than previously possible. For example, distributed processing can enable urban dynamics research to perform simulations on larger areas without making huge sacrifices in resolution. The processing can also be done in a more reasonable amount of time than with traditional single-threaded methods (a scaled version of Chester County, Pennsylvania, took about fifty days to finish its first calibration phase with a single-threaded program). This paper has several goals regarding distributed processing technology. It will describe the benefits of the technology. Real data about a distributed application will be presented as an example of the benefits that this technology can bring to USGS scientific programs. Finally, some of the issues with distributed processing that relate to USGS work will be discussed.

Open-File Report↗
USGS2023

FishPass baseline assessment of fish community assemblage and migratory patterns in in the Boardman River, Traverse City, Michigan, USA

This report on baseline assessment of fish community assemblage and migratory patterns of fishes in the lower Boardman River (LBR; Traverse City, MI (USA)) is one of four assessment projects conceived circa 2017 after the Boardman (Ottaway) River was selected by the Great Lakes Fishery Commission (GLFC) and collaborating agencies as the future site of the Selective Bi-directional Fish Passage (FishPass) project. This report describes the results from fisheries community sampling from 2017-2021 and the concurrent bio-telemetry project aimed at understanding phenological changes in the fish community and movement and space-use of a variety of large-bodied fishes in the LBR against which selective fish passage treatments will be developed and evaluated. Fish migration in riverine environments is a growing area of concern as mounting anthropogenic influences, particularly fragmentation from dams and barriers, constitute a major threat to global river species diversity. Specifically, In the Laurentian Great Lakes basin, more than 250,000 dams, weirs, culverts, and other significant obstructions prevent the movement of species both between the Great Lakes and rivers, and within rivers. Barriers impede the movement of fishes between areas critical to the completion of their lifecycle, affecting both population and ecosystem viability. However, a conundrum arises in that the same barriers can also prevent the upstream invasion of non-native or undesirable species (most notably the sea lamprey Petromyzon marinus in the Great Lakes),prevent the transfer of contaminants and diseases, halt deleterious genes, provide recreational opportunities, or generate power. As a result, fish passage solutions with the capability of selectively passing desirable taxa while restricting the dispersal of undesirable taxa (selective connectivity) are sought to solve this connectivity conundrum. FishPass is a multi-agency initiative planned to replace the Union Street Dam on the Boardman River in Traverse City,MI (USA), aimed at developing and implementing automatic or semiautomatic selective bi-directional fish guidance, sorting, and passage techniques and technologies. Pivotal to both the successful development of selective connectivity and assessment of its effects is a more complete understanding of the Boardman River’s fishery. Specifically, understanding the species and size composition of the fish community, fish movement phenology and the associated abiotic conditions. Fish community sampling confirmed the presence of 28 unique species in the LBR (Boardman River reach below Union Street Dam). Passive Integrated Transponder (PIT) tag telemetry increased the resolution of phenological shifts in the fish community that could not have been captured from periodic fish sampling. This data demonstrates large variation within species and overlap between species presence. However, discrete periods of presence were identified across most species when considering the central tendencies in the distribution of their presence. Rainbow trout Oncorhynchus mykiss were found to be omni-present in the river while brown trout Salmo trutta and smallmouth bass Micropterus dolomieu also persisted throughout a majority of the year; all of which will require continually sorting at FishPass. PIT tag telemetry also provided the important understanding that individuals (3-64%) of all species return to the LBR across multiple years. Radio telemetry (RT) proved useful in refining the entry and exit timing and in evaluating the proportion of individuals that encountered the current Union Street Dam and Kid’s Creek (the only tributary confluence below the Union Street Dam) across six species (common white sucker Catostomus commersonii, rainbow trout, smallmouth bass, walleye Sander vitreus, brown trout, and common carp Cyprinus carpio). The RT results show that these species are present in FishPass Research Publication: baseline assessment of fish community assemblage and migratory pattern in the Boardman River, Traverse City, Michigan, USA November 2023 7 between April and August. Our analysis also demonstrated that not all fish that entered the river proceeded to the Union Street Dam, but those that did, did so prior to being detected encountering Kid’s Creek. Common white sucker and rainbow trout were the only species to be detected encountering Kid’s Creek. Collectively, the results of this study provide a baseline understanding of the seasonal fish diversity and relative abundance of fishes in the LBR, and a basic description of observed movement patterns of a subset of species in the context of seasonal phenology, entry and exit behavior within the LBR, and the propensity at which telemetered individuals encounter the Union Street dam and/or Kid’s Creek.

Michigan↗
USGS2012

Practical estimates of field-saturated hydraulic conductivity of bedrock outcrops using a modified bottomless bucket method

The bottomless bucket (BB) approach (Nimmo et al., 2009a) is a cost-effective method for rapidly characterizing field-saturated hydraulic conductivity Kfs of soils and alluvial deposits. This practical approach is of particular value for quantifying infiltration rates in remote areas with limited accessibility. A similar approach for bedrock outcrops is also of great value for improving quantitative understanding of infiltration and recharge in rugged terrain. We develop a simple modification to the BB method for application to bedrock outcrops, which uses a non-toxic, quick-drying silicone gel to seal the BB to the bedrock. These modifications to the field method require only minor changes to the analytical solution for calculating Kfs on soils. We investigate the reproducibility of the method with laboratory experiments on a previously studied calcarenite rock and conduct a sensitivity analysis to quantify uncertainty in our predictions. We apply the BB method on both bedrock and soil for sites on Pahute Mesa, which is located in a remote area of the Nevada National Security Site. The bedrock BB tests may require monitoring over several hours to days, depending on infiltration rates, which necessitates a cover to prevent evaporative losses. Our field and laboratory results compare well to Kfs values inferred from independent reports, which suggests the modified BB method can provide useful estimates and facilitate simple hypothesis testing. The ease with which the bedrock BB method can be deployed should facilitate more rapid in-situ data collection than is possible with alternative methods for quantitative characterization of infiltration into bedrock.

Water Resources Research↗
USGS2000

Methods of analysis by the U.S. Geological Survey Organic Geochemistry Research Group; determination of chloroacetanilide herbicide metabolites in water using high-performance liquid chromatography-diode array detection and high-performance liquid chromatography/mass spectrometry

Analytical methods using high-performance liquid chromatography-diode array detection (HPLC-DAD) and high-performance liquid chromatography/mass spectrometry (HPLC/MS) were developed for the analysis of the following chloroacetanilide herbicide metabolites in water: acetochlor ethanesulfonic acid (ESA), acetochlor oxanilic acid (OXA), alachlor ESA, alachlor OXA, metolachlor ESA, and metolachlor OXA. Good precision and accuracy were demonstrated for both the HPLC-DAD and HPLC/MS methods in reagent water, surface water, and ground water. The mean HPLC-DAD recoveries of the chloroacetanilide herbicide metabolites from water samples spiked at 0.25, 0.50, and 2.0 mg/L (micrograms per liter) ranged from 84 to 112 percent, with relative standard deviations of 18 percent or less. The mean HPLC/MS recoveries of the metabolites from water samples spiked at 0.05, 0.20, and 2.0 mg/L ranged from 81 to 125 percent, with relative standard deviations of 20 percent or less. The limit of quantitation (LOQ) for all metabolites using the HPLC-DAD method was 0.20 mg/L, whereas the LOQ using the HPLC/MS method was 0.05 mg/L. These metabolite-determination methods are valuable for acquiring information about water quality and the fate and transport of the parent chloroacetanilide herbicides in water.

Open-File Report↗
USGS2017

A method for quantifying cloud immersion in a tropical mountain forest using time-lapse photography

Quantifying the frequency, duration, and elevation range of fog or cloud immersion is essential to estimate cloud water deposition in water budgets and to understand the ecohydrology of cloud forests. The goal of this study was to develop a low-cost and high spatial-coverage method to detect occurrence of cloud immersion within a mountain cloud forest by using time-lapse photography. Trail cameras and temperature/relative humidity sensors were deployed at five sites covering the elevation range from the assumed lifting condensation level to the mountain peaks in the Luquillo Mountains of Puerto Rico. Cloud-sensitive image characteristics (contrast, the coefficient of variation and the entropy of pixel luminance, and image colorfulness) were used with a k -means clustering approach to accurately detect cloud-immersed conditions in a time series of images from March 2014 to May 2016. Images provided hydrologically meaningful cloud-immersion information while temperature-relative humidity data were used to refine the image analysis using dew point information and provided temperature gradients along the elevation transect. Validation of the image processing method with human-judgment based classification generally indicated greater than 90% accuracy. Cloud-immersion frequency averaged 80% at sites above 900 m during nighttime hours and 49% during daytime hours, and was consistent with diurnal patterns of cloud immersion measured in a previous study. Results for the 617 m site demonstrated that cloud immersion in the Luquillo Mountains rarely occurs at the previously-reported cloud base elevation of about 600 m (11% during nighttime hours and 5% during daytime hours). The framework presented in this paper will be used to monitor at a low cost and high spatial resolution the long-term variability of cloud-immersion patterns in the Luquillo Mountains, and can be applied to ecohydrology research at other cloud-forest sites or in coastal ecosystems with advective sea fog.

El Yunque National Forest, Puerto Rico↗
USGS2025

The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models

Survival is a key life history parameter that can inform management decisions and basic life history research. Because true survival is often confounded with emigration from the study area, many studies are forced to estimate apparent survival (i.e., probability of surviving and remaining inside the study area), which can be much lower than true survival for highly mobile species. One method for estimating true survival is the Barker joint live-recapture/live-resight (JLRLR) model, which combines capture data from a study area (hereafter the ‘capture site’) with resighting data from a broader geographic area. This model assumes that live resights occur throughout the entire area where animals can disperse to and this assumption is often not met in practice. Here we use simulation to evaluate survival bias from a JLRLR model under study design scenarios that differ in the site selection for resights: global, random, fixed including the capture site, and fixed excluding the capture site. Simulation results indicate that fixed designs that included the capture site showed negative survival bias, whereas fixed designs that excluded the capture site exhibited positive survival bias. The magnitude of the bias was dependent on movement and survival, where scenarios with high survival and frequent movement had minimal bias. In an effort to help minimize bias, we developed a multistate version of the JLRLR and demonstrated reductions in survival bias compared to the single-state version for most designs. Our results suggest minimizing bias can be accomplished by: 1) using a random resight design when feasible if global sampling is not possible, 2) using the multistate JLRLR model when appropriate, 3) including the capture site in the resight sampling frame when possible, and 4) reporting survival as apparent survival if fixed sites are used for resight with the single state JLRLR model.

Peer Community Journal↗
USGS2015

Archiving California’s historical duck nesting data

The U.S. Geological Survey (USGS), in partnership with the California Waterfowl Association (CWA) and other organizations, have compiled large datasets on the nesting ecology and management of dabbling ducks and associated upland nesting birds (Northern Harriers [ Circus cyaneus ], Short-eared Owls [ Asio flammeus ], Ring-necked Pheasants [ Phasianus colchicus ], and American Bitterns [ Botaurus lentiginosus ]) throughout California on Federal Refuges, State Wildlife Areas, and private lands, some participating in State and Federal habitat programs. These datasets encompass several long-term monitoring programs at multiple sites throughout California, and include data from more than 26,000 nests and span nearly 30 years. These historical datasets represent some of the longest term datasets on nesting ducks in North America, if not the world. They are extremely valuable for ongoing waterfowl management and habitat conservation efforts in California, as well as throughout the world. However, without organization and electronic access, these data are an untapped resource and are not being used to the full extent possible. Prior to this project, these datasets were scattered among various agencies and organizations, and original paper nest cards were being stored in cardboard boxes in attics and storage containers that were not suitable for long-term archival storage. In addition, most of these data had not been entered into a computerized database and thus were at high risk for permanent data loss. To protect this irreplaceable dataset, we submitted a series of proposals to obtain funds to complete this data archival project over the past 5 years. The Central Valley Joint Venture, USGS Data Rescue Program, and USGS Ecosystems Mission Area funded this data archival project. In addition, we leveraged other USGS projects on nesting shorebirds, songbirds, and seabirds to use further resources to more fully develop the nest database structure for use on nesting waterfowl. Specifically, this large dataset on ducks was archived by USGS, but the dataset is owned and managed by a consortium of organizations. Therefore, any access and use of this data must occur through the principal investigators, who contributed data and resources to this archival project, as detailed in section, “Data Availability.” With the conclusion of this project, most duck nest data have been entered, but all nest-captured hen data and other breeding waterfowl data that were outside the scope of this project have still not been entered and electronically archived. Maintaining an up-to-date archive will require additional resources to archive and enter the new duck nest data each year in an iterative process. Further, data proofing should be conducted whenever possible, and also should be considered an iterative process as there was sometimes missing data that could not be filled in without more direct knowledge of specific projects. Despite these disclaimers, this duck data archive represents a massive and useful dataset to inform future research and management questions.

California↗
USGS2014

Connecting the dots: a collaborative USGS-NPS effort to expand the utility of monitoring data

The Natural Resource Challenge (National Park Service 1999) was a call to action. It constituted a mandate for monitoring based on the twin premises that (1) natural resources in national parks require active management and stewardship if we are to protect them from gradual degradation, and (2) we cannot protect what we do not understand. The intent of the challenge was embodied in its original description: We must expand existing inventory programs and develop efficient ways to monitor the vital signs of natural systems. We must enlist others in the scientific community to help, and also facilitate their inquiry. Managers must have and apply this information to preserve our natural resources. In this article, we report on ongoing collaborative work between the National Park Service (NPS) and the US Geological Survey (USGS) that seeks to add to our scientific understanding of the ecological processes operating behind vital signs monitoring data. The ultimate goal of this work is to provide insights that can facilitate an understanding of the systems and identify potential opportunities for active stewardship by NPS managers (Bennetts et al. 2007; Mitchell et al. 2014). The bulk of the work thus far has involved Acadia and Rocky Mountain national parks, but there are plans for extending the work to additional parks. Our story stats with work designed to consider ways of assessing the status and condition of natural resources and the potential for historical or ongoing influences of human activities. In the 1990s, the concept of "biotic integrity" began to take hold as an aspiration for developing quantitative indices describing how closely the conditions at a site resemble those found at pristine, unimpacted sites. Quantitative methods for developing indices of biotic integrity (IBIs) and elaborations of that idea (e.g., ecological integrity) have received considerable attention and application of these methods to natural resources has become widespread (Karr 1991; Barbour et al. 1999; Stoddard et al. 2008). Despite widespread use, many questions remain about how metrics are combined to form effective indices and about how to interpret both. Scientists and natural resource specialists within NPS and USGS have joined forces to critique the current analysis methods, with the collaboration involving the Rocky Mountain and Northeast Temperate NPS Inventory and Monitoring (I & M) networks, along with others, and USGS scientists from the National Wetlands Research Center and Patuxent Wildlife Research Center. Funding that initiated the project was from a joint-partnership fund managed by the USGS Ecosystems Program for National Park Monitoring research and the work was focused at Acadia National Park and Rocky Mountain National Park. Here we present synopses of two major issues addressed by the group.

The George Wright Forum↗
USGS2011

USGS global change science strategy: A framework for understanding and responding to climate and land-use change

This U.S. Geological Survey (USGS) Global Change Science Strategy expands on the Climate Variability and Change science component of the USGS 2007 Science Strategy, “Facing Tomorrow’s Challenges: USGS Science in the Coming Decade” (U.S. Geological Survey, 2007). Here we embrace the broad definition of global change provided in the U.S. Global Change Research Act of 1990 (Public Law 101–606,104 Stat. 3096–3104)—“Changes in the global environment (including alterations in climate, land productivity, oceans or other water resources, atmospheric chemistry, and ecological systems) that may alter the capacity of the Earth to sustain life”—with a focus on climate and land-use change. There are three major characteristics of this science strategy. First, it addresses the science required to broadly inform global change policy, while emphasizing the needs of natural-resource managers and reflecting the role of the USGS as the science provider for the Department of the Interior and other resource-management agencies. Second, the strategy identifies core competencies, noting 10 critical capabilities and strengths the USGS uses to overcome key problem areas. We highlight those areas in which the USGS is a science leader, recognizing the strong partnerships and effective collaboration that are essential to address complex global environmental challenges. Third, it uses a query-based approach listing key research questions that need to be addressed to create an agenda for hypothesis-driven global change science organized under six strategic goals. Overall, the strategy starts from where we are, provides a vision for where we want to go, and then describes high-priority strategic actions, including outcomes, products, and partnerships that can get us there. Global change science is a well-defined research field with strong linkages to the ecosystems, water, energy and minerals, natural hazards, and environmental health components of the USGS Science Strategy (2007). When science strategies that cover these other components are developed, coordinated implementation will be necessary to achieve Bureau-level synergies and optimize capabilities and expertise. In October 2010, USGS realigned its management and budget structure to implement its 2007 Science Strategy. The new organizational structure, in which “Global Change” is one of seven key mission areas, lends itself to the advancement of the established six strategic goals. USGS global change science is formally represented by the “Climate and Land-Use Change” Mission Area in the FY 2012 budget (USGS, 2011). This plan was developed by the USGS Global Change Science Strategy Planning Team (SSPT) appointed by the USGS Director on March 4, 2010 and charged with developing a Global Change Science Strategy for the coming decade (McNutt, 2010). USGS managers and science staff are the main audience for this science strategy. This document is also intended to serve as the foundation for consistent USGS collaboration and communication with partners and stakeholders.

Open-File Report↗
USGS2012

Development of a real-time PCR assay for detection of planktonic red king crab ( Paralithodes camtschaticus (Tilesius 1815)) larvae

The Alaskan red king crab ( Paralithodes camtschaticus ) fishery was once one of the most economically important single-species fisheries in the world, but is currently depressed. This fishery would benefit from improved stock assessment capabilities. Larval crab distribution is patchy temporally and spatially, requiring extensive sampling efforts to locate and track larval dispersal. Large-scale plankton surveys are generally cost prohibitive because of the effort required for collection and the time and taxonomic expertise required to sort samples to identify plankton individually via light microscopy. Here, we report the development of primers and a dual-labeled probe for use in a DNA-based real-time polymerase chain reaction assay targeting the red king crab, mitochondrial gene cytochrome oxidase I for the detection of red king crab larvae DNA in plankton samples. The assay allows identification of plankton samples containing crab larvae DNA and provides an estimate of DNA copy number present in a sample without sorting the plankton sample visually. The assay was tested on DNA extracted from whole red king crab larvae and plankton samples seeded with whole larvae, and it detected DNA copies equivalent to 1/10,000th of a larva and 1 crab larva/5mL sieved plankton, respectively. The real-time polymerase chain reaction assay can be used to screen plankton samples for larvae in a fraction of the time required for traditional microscopial methods, which offers advantages for stock assessment methodologies for red king crab as well as a rapid and reliable method to assess abundance of red king crab larvae as needed to improve the understanding of life history and population processes, including larval population dynamics.

Journal of Shellfish Research↗
USGS2018

Bioactive contaminants of emerging concern in National Park waters of the northern Colorado Plateau, USA

Pharmaceuticals and personal care products (PPCPs), wastewater indicators (WWIs), and pesticides (herein, Contaminants of Emerging Concern [CECs]) have been documented in surface waters throughout the world and have associated risks to aquatic life. While much research has focused on temperate and urbanized watersheds, less is known about CEC presence in semi-arid landscapes, where water availability is limited and populations are low. CEC presence in water and sediment is reported for 21 sites in eight U.S. national parks in the northern Colorado Plateau region. From 2012 to 2016, at least one PPCP and/or WWI was detected at most sites on over half of sampling visits, indicating that CECs are not uncommon even in isolated areas. CEC detections were generally fewer and at lower concentrations than in urbanized or agricultural watersheds. Consistent with studies from other U.S. regions, the most frequently detected CECs in this study include DEET, caffeine, organophosphorus flame retardants, and bisphenol A in water and fecal indicators and polycyclic aromatic hydrocarbons in sediment. Maximum concentrations in this study were generally below available water quality benchmarks, sediment quality guidelines, and risk assessment thresholds associated with vertebrates. Additional work is needed to assess the potential activity of hormones, which had high reporting limits in our study, and potential bioactivity of environmental concentrations for invertebrates, microbial communities, and algae. Potential sources of CEC contamination include upstream wastewater effluent discharges and National Park Service invasive-plant-control herbicide applications. CEC occurrence patterns and similarities between continuous and isolated flow locations suggest that direct contamination from individual visitors may also occur. While our data indicate there is little aquatic health risk associated with CECs at our sites, our results demonstrate the ubiquity of CECs on the landscape and a continued need for public outreach concerning resource-use ethics and the potential effects of upstream development.

Colorado Plateau↗
USGS2002

Predators

Calving caribou ( Rangifer tarandus ) of the Central Arctic herd, Alaska, have avoided the infrastructure associated with the complex of petroleum development areas from Prudhoe Bay to Kuparuk (Cameron et al. 1992, Nellemann and Cameron 1998, and Section 4 of this document). Calving females of the Porcupine caribou herd may similarly avoid any oil field roads and pipelines developed in areas traditionally used during the calving and post-calving periods. This may displace the caribou females and calves to areas east and south of the 1002 Area of the Arctic National Wildlife Refuge. Increased calf mortality could occur if calving caribou are displaced into areas that have a higher density of predators, higher rates of predation, or where a higher proportion of the predators regularly use caribou as a food source (Whitten et al. 1992). Our study assessed predation risks to caribou calving in the 1002 Area versus calving in potential displacement areas. Due to funding constraints, our research focused on grizzly bears ( Ursus arctos ), with wolves (Camus lupus) and golden eagles ( Aquila chrysaetos ) receiving only cursory attention. Our research objectives were 1) to compare relative abundance of predators within the 1002 Area with that in adjacent peripheral areas, 2) to determine factors affecting predator abundance on the calving grounds, and 3) to quantify the use of caribou as a food source for predators and the importance of caribou to the productivity of predator populations using the coastal plain of the Arctic National Wildlife Refuge.

Alaska, Northwest Territories, Yukon Territory↗
USGS1989

Assessing the relationship between Section 404 and wetland losses: a feasibility study

The primary objective of the Clean Water Act of 1977 (33 U.S.C. 1251) is to restore and maintain the physical, chemical, and biological integrity of the Nation's waters. Section 404 of the Act regulates the discharge of dredged or fill materials into wetlands and represents the primary Federal authority for regulation of wetland alterations. Since its inception, the Section 404 program has been controversial in regard to the extent to which it was intended to provide wetlands regulation. Section 404 requires those who wish to discharge dredged or fill material into waters of the United States, which include many wetlands, to first obtain a Federal permit. The Environmental Protection Agency (EPA) has overall responsibility for administration of the Section 404 program and promulgates guidelines that must be followed in issuing permits. In addition, EPA has the final authority to prohibit specific discharges if the environmental impacts are unacceptable. The U.S. Army Corps of Engineers (Corps) issues Section 404 permits, which can be of two types. Individual Permits are issued following case-by-case reviews of proposed discharges. General Permits, which can be either nationwide or regional in scope, are authorized by the Corps for categories of activities that are similar in nature and that have only minimal individual and cumulative adverse environmental impacts. EPA, the National Marine Fisheries Service (NMFS), the Fish and Wildlife Service (Service), and State natural resource agencies review and comment on permit applications and offer recommendations on appropriate mitigation measures. Although comments from the Service and other natural resource agencies are advisory in nature (EPA's veto authority excepted), they can serve as the basis for modifying, conditioning, or denying a Section 404 permit. In 1986, in a survey conducted by the National Ecology Research Center, Service personnel indicated interest in additional information concerning both wetland trends and the impacts of activities authorized by the Corps under Section 404 (Roelle 1986). Although there is some information concerning wetland losses for certain geographic areas and for the Nation as a whole (Frayer et al. 1983; Tiner 1984), there appears to be little information on how these losses relate to the Section 404 permitting process. The primary objective of this study was to determine the feasibility of estimating wetland losses in relationship to Individual and General Permits issued under Section 404. A secondary objective was to assemble data on acceptance and implementation of specific mitigation recommendations offered by the Service and other natural resource agencies in connection with development activities on wetlands examined. At present, 26 categories of Nationwide permits have been authorized by the Corps. Nationwide permit 26 was of particular interest in this study because it specifically authorizes discharges into wetlands under certain circumstances (see Figure 1 and related text for a more complete discussion of circumstances under which Nationwide Permit 26 is applicable). All subsequent references to Nationwide or General permits pertain to Nationwide Permit 26.

Report↗
USGS2010

Strategic Science for Coral Ecosystems 2007-2011

Shallow and deep coral ecosystems are being imperiled by a combination of stressors. Climate change, unsustainable fishing practices, and disease are transforming coral communities at regional to global scales. At local levels, excessive amounts of sediments, nutrients, and contaminants are also impacting the many benefits that healthy coral ecosystems provide. This Plan, Strategic Science for Coral Ecosystems, describes the information needs of resource managers and summarizes current research being conducted by U.S. Geological Survey (USGS) scientists and partners. It outlines important research actions that need to be undertaken over the next five years to achieve more accurate forecasting of future conditions and develop more effective decision-support tools to adaptively manage coral ecosystems. The overarching outcome of this Plan, if fully implemented, would be in transferring relevant knowledge to decision-makers, enabling them to better protect and sustain coral ecosystem services. These services include sources of food, essential habitat for fisheries and protected species, protection of coastlines from wave damage and erosion, recreation, and cultural values for indigenous communities. The USGS has a long history of research and monitoring experience in studying ancient and living coral communities and serving many stakeholders. The research actions in this Plan build on the USGS legacy of conducting integrated multidisciplinary science to address complex environmental issues. This Plan is responsive to Federal legislation and authorities and a variety of external and internal drivers that include the President's Ocean Action Plan, the recommendations of the Coral Reef Task Force, the information needs of Bureaus in the Department of Interior, the USGS Bureau Science Strategy (USGS 2007) and the formal plans of several USGS Programs. To achieve this Plan's desired outcomes will require increased funding and more effective coordination and collaboration among USGS managers and scientists within a national and international framework of partnerships in coral ecosystem science.

Circular↗
USGS2002

Mexican native trouts: A review of their history and current systematic and conservation status

While biologists have been aware of the existence of native Mexican trouts for over a century, they have received little study. The few early studies that did much more than mention their existence began in the 1930s and continued into the early 1960s, focusing primarily on distributional surveys and taxonomic analyses. Starting in the 1980s the Baja California rainbow trout became the subject of more detailed studies, but very little remains known of mainland trouts of the Sierra Madre Occidental. We review earlier studies and report on our own collections and observations made between 1975 and 2000. We present newly discovered historical evidence that leads us to conclude that a "lost" cutthroat trout, a lineage not previously known from Mexico, was collected more than a century ago from headwaters of the Ri??o Conchos (a major tributary of the Rio Grande (= Ri??o Bravo)), a basin not previously considered to harbor a native trout. We review the last century of regional natural resource management and discuss our own observations of trout habitats. Impacts of logging, road building and overgrazing are widespread and expanding. Many streams suffer from heavy erosion, siltation and contamination, and though long-term hydrologic data are generally not available, there is evidence of decreased discharge in many streams. These problems appear related to region-wide land management practices as well as recent regional drought. Trout culture operations using exotic rainbow trout have rapidly proliferated throughout the region, threatening genetic introgression and/or competition with native forms and predation on them. Knowledge of distribution, abundance, relationships and taxonomy, not to mention ecology and population biology, of native trouts of the Sierra Madre Occidental remains inadequate. Vast areas of most mainland drainages are still unexplored by fish collectors, and even rudimentary information regarding basic biology, ecology and population structure of stocks remains lacking. Concentrated exploration, research and management of this long overlooked and undervalued resource are all urgently needed. The history of natural resources exploitation that placed so many native trouts of the western United States on threatened and endangered species lists is repeating itself in the Sierra Madre Occidental. Without concentrated action and development of region-wide socio-economic solutions for current, largely non-sustainable resource management practices, native Mexican trout gene pools will soon be in grave danger of extinction.

Reviews in Fish Biology and Fisheries↗