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Results for “Diversity and Distributions”

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At least 1,081 records · Page 60Linked to original sources
USGS2021

Exploring the potential of electrospray-Orbitrap for stable isotope analysis using nitrate as a model

Widely used isotope ratio mass spectrometers have limited capabilities to measure metabolites, drugs, or small polyatomic ions without the loss of structural isotopic information. A new approach has recently been introduced that uses electrospray ionization Orbitrap to measure multidimensional isotope signatures of intact polar compounds. Using nitrate as a model compound, this study aims to establish performance metrics for comparisons with conventional IRMS at the natural abundance level. We present a framework on how to convert isotopolog intensities to δ values that are commonly used in the isotope geochemistry community. The quantification of seven nitrate isotopologs provides multiple pathways for obtaining the primary N and O δ values including non-mass-dependent O isotope variations, as well as opportunities to explore nonrandom isotopic distributions (i.e., clumping effects) within molecular nitrate. Using automation and the adaptation of measurement principles that are specific to isotope ratio analysis, nitrate δ15NAIR, δ18OVSMOW, and δ17OVSMOW were measured with a long-term precision of 0.4‰ or better for isotopic reference materials and purified nitrate from environmental samples. In addition, we demonstrate promising results for unpurified environmental samples in liquid form. With these new developments, this study connects the two largely disparate mass spectrometry fields of bioanalytical MS and isotope ratio MS, thus providing a route to measure new isotopic signatures in diverse organic and inorganic solutes.

Analytical Chemistry↗
USGS2015

Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated from two three-hour runs on the Ion Torrent PGM can generate a sufficient number of nuclear and mitochondrial markers to improve understanding of the evolutionary and ecological dynamics of non-model and in particular, invasive species.

European Russia↗
USGS2023

Alerting the globe of consequential earthquakes

The primary ingredients on the hazard side of the equation include the rapid characterization of the earthquake source and quantifying the spatial distribution of the shaking, plus any secondary hazards an earthquake may have triggered. On the earthquake impact side, loss calculations require the aforementioned hazard assessments—and their uncertainties—as input, plus the quantification of the exposure and vulnerability of structures, infrastructure, and the affected inhabitants. Lastly, effectively communicating uncertain estimates of the resulting impacts on society requires careful consideration of its function and form. All these aspects of rapid earthquake information delivery entailed wide-ranging collaborative research and development among seismologists, earthquake engineers, geographers, social scientists, Information Technology professionals, and communication experts, leveraging diverse components and ingredients not achievable without extensive collaboration. I was very fortunate to be able to work on interesting and useful projects with many colleagues who got involved with them. Advances in content, its rapid delivery, and our ability to better communicate uncertain loss estimates greatly expanded the range of users and critical decision-makers who could directly benefit from rapid post-earthquake information. Moreover, in the critical user–developer feedback loop, we have intently followed requests from users to develop new ways of delivering the most-requested post-earthquake information within the limitations of the science and technology. Such new avenues and tools then motivated and prioritized additional research directions and developments.

Perspectives of Earth and Space Scientists↗
USGS2023

Serum virome of southern Beaufort Sea polar bears (Ursus maritimus) during a period of rapid climate change

Climate change affects the behavior, physiology and life history of many Arctic wildlife species. It can also influence the distribution and ecology of infectious agents. The southern Beaufort Sea (SB) subpopulation of polar bears ( Ursus maritimus ) has experienced dramatic behavioral changes due to retreating sea ice and other climate-related factors, but the effects of these changes on physiology and infection remain poorly understood. Using serum from polar bears sampled between 2004 and 2015 and metagenomic DNA sequencing, we identified 48 viruses, all of the family Anelloviridae . Anelloviruses are small, ubiquitous infectious agents with circular single-stranded DNA genomes that are not known to cause disease but, in humans, covary in diversity and load with immunological compromise. We therefore examined the usefulness of anelloviruses as biomarkers of polar bear physiological stress related to climate and habitat use. Polar bear anelloviruses sorted into two distinct clades on a phylogenetic tree, both of which also contained anelloviruses of giant pandas ( Ailuropoda melanoleuca ), another ursid. Neither anellovirus diversity nor load were associated with any demographic variables, behavioral factors or direct physiological measures. However, pairwise genetic distances between anelloviruses were positively correlated with pairwise differences in sampling date, suggesting that the polar bear “anellome”is evolving over time. These findings suggest that anelloviruses are not a sensitive indicator of polar physiological stress, but they do provide a baseline for evaluating future changes to polar bear viromes.

Alaska↗
USGS1997

Demersal fish assemblages of the northeastern Chukchi Sea, Alaska

We documented the distribution and abundance of demersal fishes in the northeastern Chukchi Sea, Alaska, in 1990 and 1991, and described 1990 demersal fish assemblages and their relationship to general oceanographic features in the area. We collected samples using an otter trawl at 48 stations in 1990 and 16 in 1991, and we identified a total of 66 species in 14 families. Gadids made up 83% and 69% of the abundance in 1990 and 1991, respectively. Cottids, pleuronectids, and zoarcids together made up 15% of the species in 1990, 28% in 1991. The number of species, species diversity (H), and evenness (V') generally were greater inshore than offshore and greater in the south than in the north. There were significant differences in ranks of species, species diversity, and evenness at 3 of 8 stations sampled beth years. From data collected in 1990, 3 nearshore and 3 offshore station groupings were defined. The northern offshore assemblages had the fewest species, lowest diversity and evenness, and least abundance, whereas two southern assemblages had the most species, highest diversity and evenness, and greatest abundance. We determined that bottom salinity and percent gravel were probably the primary factors influencing assemblage arrangement.

Fishery Bulletin↗
USGS2022

Parameterizing an aeolian erosion model for rangelands

Aeolian processes are fundamental to arid and semi-arid ecosystems, but modeling approaches are poorly developed for assessing impacts of management and environmental change on sediment transport rates over meaningful spatial and temporal scales. For model estimates to provide value, estimates of sediment flux that encapsulate intra- and inter-annual and spatial variability are needed. Further, it is important to quantify and communicate transparent estimates of model uncertainty to users. Here, we present a wind erosion and dust emission model parameterized for rangelands using a Generalized Likelihood Uncertainty Estimation framework. Modeled horizontal sediment flux was calibrated using data from five diverse grassland and shrubland sites from the USDA National Wind Erosion Research Network. Observations of wind speed, vegetation height, length of gaps between vegetation, and percent bare ground were used as model inputs. Horizontal sediment flux estimates from 10,000 independently selected parameter sets were compared to flux observations from 44 ∼ month-long collection periods to calculate a likelihood measure for each model. Results show good agreement for individual sampling periods across sites with few observations falling outside prediction bounds and a one-to-one relationship between median predictions and observations. Additionally, combined distributions of sediment flux estimates from all sample periods for a given site closely approximated the probability of observing a given flux at that site. These results suggest AERO effectively represents temporal variability in aeolian transport rates at rangeland sites and provides robust assessments suitable for assessing land health and better predicting changes in air quality and the impacts of land management activities.

Aeolian Research↗
USGS2011

Habitat diversity in the Northeastern Gulf of Mexico: Selected video clips from the Gulfstream Natural Gas Pipeline digital archive

This project combines underwater video with maps and descriptions to illustrate diverse seafloor habitats from Tampa Bay, Florida, to Mobile Bay, Alabama. A swath of seafloor was surveyed with underwater video to 100 meters (m) water depth in 1999 and 2000 as part of the Gulfstream Natural Gas System Survey. The U.S. Geological Survey (USGS) in St. Petersburg, Florida, in cooperation with Eckerd College and the Florida Department of Environmental Protection (FDEP), produced an archive of analog-to-digital underwater movies. Representative clips of seafloor habitats were selected from hundreds of hours of underwater footage. The locations of video clips were mapped to show the distribution of habitat and habitat transitions. The numerous benthic habitats in the northeastern Gulf of Mexico play a vital role in the region's economy, providing essential resources for tourism, natural gas, recreational water sports (fishing, boating, scuba diving), materials, fresh food, energy, a source of sand for beach renourishment, and more. These submerged natural resources are important to the economy but are often invisible to the general public. This product provides a glimpse of the seafloor with sample underwater video, maps, and habitat descriptions. It was developed to depict the range and location of seafloor habitats in the region but is limited by depth and by the survey track. It should not be viewed as comprehensive, but rather as a point of departure for inquiries and appreciation of marine resources and seafloor habitats. Further information is provided in the Resources section.

Florida;Alabama;Mississippi;Louisiana↗
USGS2024

Identifying the forage base and critical forage taxa for Chesapeake waterbirds

To effectively maximize the conservation value of management plans intended to capture ecosystem-wide health, it is essential to obtain an understanding of emergent patterns in dietary dynamics spanning many species. Chesapeake Bay, USA, is a critical ecosystem used annually by a diverse assortment of waterbird species, including several of conservation concern. However, the ecosystem is threatened by many ecological pressures driven largely by the dense human population of the surrounding region. These issues necessitate proactive monitoring and management efforts to track the health of ecosystems like the Chesapeake Bay. Such monitoring efforts of population dynamics require adequate data on the connections between trophic levels to understand how changes to the forage base might influence higher trophic levels, such as these diverse avian predators. However, we have historically lacked standardized quantitative data drawing these connections at the community level, as well as the relative importance of these taxa in the diet of such predators. We collated existing quantitative data on avian dietary composition to construct a database on the diets of 58 waterbird species that make use of the Chesapeake Bay. From this database, we quantified the relative importance of forage taxa to the diet of each waterbird species. Such data can enable managers to develop a comprehensive suite of forage taxa indicators whose abundance and distributions can be monitored as a proxy for ecosystem health. It is our goal that this database be harnessed as a tool to enable conservation practitioners to prioritize indicator taxa for monitoring purposes, contributing towards conservation plans that best address the health of the ecosystem at large.

Delaware, Maryland, Virginia↗
USGS2022

Post-landing major element quantification using SuperCam laser induced breakdown spectroscopy

The SuperCam instrument on the Perseverance Mars 2020 rover uses a pulsed 1064 nm laser to ablate targets at a distance and conduct laser induced breakdown spectroscopy (LIBS) by analyzing the light from the resulting plasma. SuperCam LIBS spectra are preprocessed to remove ambient light, noise, and the continuum signal present in LIBS observations. Prior to quantification, spectra are masked to remove noisier spectrometer regions and spectra are normalized to minimize signal fluctuations and effects of target distance. In some cases, the spectra are also standardized or binned prior to quantification. To determine quantitative elemental compositions of diverse geologic materials at Jezero crater, Mars, we use a suite of 1198 laboratory spectra of 334 well-characterized reference samples. The samples were selected to span a wide range of compositions and include typical silicate rocks, pure minerals (e.g., silicates, sulfates, carbonates, oxides), more unusual compositions (e.g., Mn ore and sodalite), and replicates of the sintered SuperCam calibration targets (SCCTs) onboard the rover. For each major element (SiO 2 , TiO 2 , Al 2 O 3 , FeO T , MgO, CaO, Na 2 O, K 2 O), the database was subdivided into five “folds” with similar distributions of the element of interest. One fold was held out as an independent test set, and the remaining four folds were used to optimize multivariate regression models relating the spectrum to the composition. We considered a variety of models, and selected several for further investigation for each element, based primarily on the root mean squared error of prediction (RMSEP) on the test set, when analyzed at 3 m. In cases with several models of comparable performance at 3 m, we incorporated the SCCT performance at different distances to choose the preferred model. Shortly after landing on Mars and collecting initial spectra of geologic targets, we selected one model per element. Subsequently, with additional data from geologic targets, some models were revised to ensure results that are more consistent with geochemical constraints. The calibration discussed here is a snapshot of an ongoing effort to deliver the most accurate chemical compositions with SuperCam LIBS.

Spectrochimica Acta B↗
USGS2011

Globally Gridded Satellite observations for climate studies

Geostationary satellites have provided routine, high temporal resolution Earth observations since the 1970s. Despite the long period of record, use of these data in climate studies has been limited for numerous reasons, among them that no central archive of geostationary data for all international satellites exists, full temporal and spatial resolution data are voluminous, and diverse calibration and navigation formats encumber the uniform processing needed for multisatellite climate studies. The International Satellite Cloud Climatology Project (ISCCP) set the stage for overcoming these issues by archiving a subset of the full-resolution geostationary data at ~10-km resolution at 3-hourly intervals since 1983. Recent efforts at NOAA's National Climatic Data Center to provide convenient access to these data include remapping the data to a standard map projection, recalibrating the data to optimize temporal homogeneity, extending the record of observations back to 1980, and reformatting the data for broad public distribution. The Gridded Satellite (GridSat) dataset includes observations from the visible, infrared window, and infrared water vapor channels. Data are stored in Network Common Data Format (netCDF) using standards that permit a wide variety of tools and libraries to process the data quickly and easily. A novel data layering approach, together with appropriate satellite and file metadata, allows users to access GridSat data at varying levels of complexity based on their needs. The result is a climate data record already in use by the meteorological community. Examples include reanalysis of tropical cyclones, studies of global precipitation, and detection and tracking of the intertropical convergence zone.

Bulletin of the American Meteorological Society↗
USGS2016

The persistence and characteristics of Chinook salmon migrations to the Upper Klamath River prior to exclusion by dams

In this research article, John Hamilton and his co-authors present extensive new research and information gathered since a 2005 publication on the historical evidence of anadromomous fish distribution in the Upper Klamath River watershed. Using historical accounts from early explorers and ethnographers to early-twentieth-century photographs, newspaper accounts, and government reports, the authors provide a more complete record of past salmon migrations. The updated record “substantiate[s] the historical persistence of salmon, their migration characteristics, and the broad population baseline that will be key to future commercial, recreational, and Tribal fisheries in the Klamath River and beyond.” During a time when salmon restoration plans are being considered in the region, the historical record can serve as guidance to once again establish diverse and thriving populations.

California, Oregon↗
USGS2023

Space-based Earth observation and ecosystem extent: Exploring opportunities

The purpose of this white paper is to explore and communicate potential new opportunities for using space-based Earth observation (EO) for monitoring biodiversity with a focus on ecosystem extent (the distribution of ecosystems on the Earth). It is part of a new activity of the Committee on Earth Observation Satellites (CEOS), a collaboration of the world’s space agencies that facilitates cross-agency coordination of EO. This activity, now manifested as the CEOS Ecosystem Extent Task Team, is focused on increasing the CEOS role in biodiversity applications, initially using ecosystem extent as a vehicle for discussion and exploration of ideas. The audience is two-fold: CEOS Principals that represent their agency, and the biodiversity community with a particular focus on the Convention on Biological Diversity (CBD) and their Parties as well as the UN System of Environmental-Economic Accounting (UN SEEA).

Report↗
USGS2024

Using mobile acoustic monitoring and false-positive N-mixture models to estimate bat abundance and population trends

Estimating the abundance of unmarked animal populations from acoustic data is challenging due to the inability to identify individuals and the need to adjust for observation biases including detectability (false negatives), species misclassification (false positives), and sampling exposure. Acoustic surveys conducted along mobile transects were designed to avoid counting individuals more than once, where raw counts are commonly treated as an index of abundance. More recently, false-positive abundance models have been developed to estimate abundance while accounting for imperfect detection and misclassification. We adapted these methods to model summertime abundance and trends of three species of bats at multiple spatial scales using acoustic recordings collected along mobile transects by partners of the North American Bat Monitoring Program (NABat) from 2012 to 2020. This multiscale modeling spanned individual transect routes, larger NABat grid cells (10 km × 10 km), and across the entire extent of modeled species ranges. We estimated relationships between species abundances and a suite of abiotic and biotic predictors (landcover types, climatological variables, physiographic diversity, building density, and the impacts of white-nose syndrome [WNS]) and found varying levels of support between species. We present clear evidence of substantial declines in populations of tricolored bats ( Perimyotis subflavus ) and little brown bats ( Myotis lucifugus ), declines that corresponded in space and time with the progression of WNS, a devastating disease of hibernating bats. In contrast, our analysis revealed that similar population-wide declines probably have not occurred in big brown bats ( Eptesicus fuscus ), a species known to be less affected by WNS. This study provides the first abundance-based species distribution predictions and population trends for bats in their summer ranges in North America. These models will probably be applicable to assessing wildlife populations in other monitoring programs where acoustic data are used or where false-negative and false-positive detections are present. Finally, our abundance framework (as a spatial point pattern process) can serve as a foundation from which more sophisticated integrated species distribution models that incorporate additional streams of monitoring data (e.g., stationary acoustics, captures) can be developed for North American bats.

Ecological Monographs↗
USGS1981

Ridges and scarps in the equatorial belt of Mars

The morphology and distribution of ridges and scarps on Mars in the ± 30° latitude belt were investigated. Two distinct types of ridges were recognized. The first is long and linear, resembling mare ridges on the Moon; it occurs mostly in plains areas. The other is composed of short, anastomosing segments and occurs mostly in ancient cratered terrain and intervening plateaus. Where ridges are eroded, landscape configurations suggest that they are located along regional structures. The age of ridges is uncertain, but some are as young as the latest documented volcanic activity on Mars. The origins of ridges are probably diverse-they may result from wrinkling due to compression or from buckling due to settling over subsurface structures. The similar morphologic expressions of ridge types of various origins may be related to a similar deformation mechanism caused by two main factors: (1) most ridges are developed in thick layers of competent material and (2) ridges formed under stresses near a free surface.

The Moon and the Planets↗
USGS2011

Prototyping an online wetland ecosystem services model using open model sharing standards

Great interest currently exists for developing ecosystem models to forecast how ecosystem services may change under alternative land use and climate futures. Ecosystem services are diverse and include supporting services or functions (e.g., primary production, nutrient cycling), provisioning services (e.g., wildlife, groundwater), regulating services (e.g., water purification, floodwater retention), and even cultural services (e.g., ecotourism, cultural heritage). Hence, the knowledge base necessary to quantify ecosystem services is broad and derived from many diverse scientific disciplines. Building the required interdisciplinary models is especially challenging as modelers from different locations and times may develop the disciplinary models needed for ecosystem simulations, and these models must be identified and made accessible to the interdisciplinary simulation. Additional difficulties include inconsistent data structures, formats, and metadata required by geospatial models as well as limitations on computing, storage, and connectivity. Traditional standalone and closed network systems cannot fully support sharing and integrating interdisciplinary geospatial models from variant sources. To address this need, we developed an approach to openly share and access geospatial computational models using distributed Geographic Information System (GIS) techniques and open geospatial standards. We included a means to share computational models compliant with Open Geospatial Consortium (OGC) Web Processing Services (WPS) standard to ensure modelers have an efficient and simplified means to publish new models. To demonstrate our approach, we developed five disciplinary models that can be integrated and shared to simulate a few of the ecosystem services (e.g., water storage, waterfowl breeding) that are provided by wetlands in the Prairie Pothole Region (PPR) of North America.

Environmental Modelling and Software↗
USGS2013

A Sr-Nd isotopic study of sand-sized sediment provenance and transport for the San Francisco Bay coastal system

A diverse suite of geochemical tracers, including 87 Sr/ 86 Sr and 143 Nd/ 144 Nd isotope ratios, the rare earth elements (REEs), and select trace elements were used to determine sand-sized sediment provenance and transport pathways within the San Francisco Bay coastal system. This study complements a large interdisciplinary effort (Barnard et al., 2012) that seeks to better understand recent geomorphic change in a highly urbanized and dynamic estuarine-coastal setting. Sand-sized sediment provenance in this geologically complex system is important to estuarine resource managers and was assessed by examining the geographic distribution of this suite of geochemical tracers from the primary sources (fluvial and rock) throughout the bay, adjacent coast, and beaches. Due to their intrinsic geochemical nature, 143 Nd/ 144 Nd isotopic ratios provide the most resolved picture of where sediment in this system is likely sourced and how it moves through this estuarine system into the Pacific Ocean. For example, Nd isotopes confirm that the predominant source of sand-sized sediment to Suisun Bay, San Pablo Bay, and Central Bay is the Sierra Nevada Batholith via the Sacramento River, with lesser contributions from the Napa and San Joaquin Rivers. Isotopic ratios also reveal hot-spots of local sediment accumulation, such as the basalt and chert deposits around the Golden Gate Bridge and the high magnetite deposits of Ocean Beach. Sand-sized sediment that exits San Francisco Bay accumulates on the ebb-tidal delta and is in part conveyed southward by long-shore currents. Broadly, the geochemical tracers reveal a complex story of multiple sediment sources, dynamic intra-bay sediment mixing and reworking, and eventual dilution and transport by energetic marine processes. Combined geochemical results provide information on sediment movement into and through San Francisco Bay and further our understanding of how sustained anthropogenic activities which limit sediment inputs to the system (e.g., dike and dam construction) as well as those which directly remove sediments from within the Bay, such as aggregate mining and dredging, can have long-lasting effects

California↗
USGS1998

Evidence for buoyancy regulation as a speciation mechanism in Great Lakes ciscoes

We present evidence for a hypothesis that the deepwater ciscoes ( Coregonus spp.) of the Laurentian Great Lakes were selected for buoyancy-regulation traits that facilitated planktivory on Mysis relict , a crustacean that undertakes extensive diel vertical migration (DVM). We assessed the vertical distribution and behavior of bloaters ( C. hoyi ) in Lake Michigan with bottom and mid-water trawls in late summer 1987 and with acoustics in August 1995. Biomass of bloaters on the lake bottom was reduced by 84% at night. Mean size of bloaters increased with depth as did the reduction in night biomass. Juvenile bloaters (<160 mm total length) occurred in both warm surface waters and in the hypolimnion where adults were aggregated. Hypolimnetic bloaters were 10 to 50 m above the bottom at night, but DVM was confined to the hypolimnion. The greater historical species diversity of deepwater ciscoes in Lakes Michigan and Huron compared with Lake Superior may be a function of reduced availability of mysids in Lake Superior.

Book chapter↗
USGS2014

Distribution and transmission of the highly pathogenic parasite Ichthyophonus in marine fishes of Alaska

A combination of field surveys, molecular typing, and laboratory experiments were used to improve our understanding of the distribution and transmission mechanisms of fish parasites in the genus Ichthyophonus . Ichthyophonus spp. infections were detected from the Bering Sea to the coast of Oregon in 10 of 13 host species surveyed. Sequences of rDNA extracted from these isolates indicate that a ubiquitous Ichthyophonus type occurs in the NE Pacific Ocean and Bering Sea and accounts for nearly all the infections encountered. Among NE Pacific isolates, only parasites from yellowtail rockfish and Puget Sound rockfish varied at the DNA locus examined. These data suggest that a single source population of these parasites is available to fishes in diverse niches across a wide geographic range. A direct life cycle within a common forage species could account for the relatively low parasite diversity we encountered. In the laboratory we tested the hypothesis that waterborne transmission occurs among Pacific herring, a common NE Pacific forage species. No horizontal transmission occurred during a four-month cohabitation experiment involving infected herring and conspecific sentinels. The complete life cycle of Ichthyophonus spp. is not known, but these results suggest that system-wide processes maintain a relatively homogenous parasite population.

Report↗