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At least 829 records · Page 46Linked to original sources

USGS1989

Adaptive modeling, identification, and control of dynamic structural systems. I. Theory

A concise review of the fheory of adaptive modeling, identification, and control of dynamic structural systems based on discrete‐time recordings is presented. Adaptive methods have four major advantages over the classical methods: (1) Removal of the noise from the signal is done over the whole frequency band; (2) time‐varying characteristics of systems can be tracked; (3) systems with unknown characteristics can be controlled; and (4) a small segment of the data is needed during the computations. Included in the paper are the discrete‐time representation of single‐input single‐output (SISO) systems, models for SISO systems with noise, the concept of stochastic approximation, recursive prediction error method (RPEM) for system identification, and the adaptive control. Guidelines for model selection and model validation and the computational aspects of the method are also discussed in the paper. The present paper is the first of two companion papers. The theory given in the paper is limited to that which is necessary to follow the examples for applications in structural dynamics presented in the second paper.

Journal of Engineering Mechanics↗

USGS2008

Temporal and spatial structure in a daily wildfire-start data set from the western United States (198696)

The temporal and spatial structure of 332 404 daily fire-start records from the western United States for the period 1986 through 1996 is illustrated using several complimentary visualisation techniques. We supplement maps and time series plots with Hovmo??ller diagrams that reduce the spatial dimensionality of the daily data in order to reveal the underlying space?time structure. The mapped distributions of all lightning- and human-started fires during the 11-year interval show similar first-order patterns that reflect the broad-scale distribution of vegetation across the West and the annual cycle of climate. Lightning-started fires are concentrated in the summer half-year and occur in widespread outbreaks that last a few days and reflect coherent weather-related controls. In contrast, fires started by humans occur throughout the year and tend to be concentrated in regions surrounding large-population centres or intensive-agricultural areas. Although the primary controls of human-started fires are their location relative to burnable fuel and the level of human activity, spatially coherent, weather-related variations in their incidence can also be noted. ?? IAWF 2008.

International Journal of Wildland Fire↗

USGS1994

Community structure of a microbial mat: The phylogenetic dimension

Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat.

Proceedings of the National Academy of Sciences of↗

USGS2015

Spatial structure of morphological and neutral genetic variation in Brook Trout

Brook Trout Salvelinus fontinalis exhibit exceptional levels of life history variation, remarkable genetic variability, and fine-scale population structure. In many cases, neighboring populations may be highly differentiated from one another to an extent that is comparable with species-level distinctions in other taxa. Although genetic samples have been collected from hundreds of populations and tens of thousands of individuals, little is known about whether differentiation at neutral markers reflects phenotypic differences among Brook Trout populations. We compared differentiation in morphology and neutral molecular markers among populations from four geographically proximate locations (all within 24 km) to examine how genetic diversity covaries with morphology. We found significant differences among and/or within streams for all three morphological axes examined and identified the source stream of many individuals based on morphology (52.3% classification efficiency). Although molecular and morphological differentiation among streams ranged considerably (mean pairwise F ST : 0.023–0.264; pairwise P ST : 0.000–0.339), the two measures were not significantly correlated. While in some cases morphological characters appear to have diverged to a greater extent than expected by neutral genetic drift, many traits were conserved to a greater extent than were neutral genetic markers. Thus, while Brook Trout exhibit fine-scale spatial patterns in both morphology and neutral genetic diversity, these types of biological variabilities are being structured by different ecological and evolutionary processes. The relative influences of genetic drift versus selection and phenotypic plasticity in shaping morphology appear to vary among populations occupying nearby streams.

Maryland↗

USGS2015

Patterns of fish assemblage structure and habitat use among main- and side-channel environments in the lower Kootenai River, Idaho

The lower Kootenai River, Idaho, was sampled during the summers of 2012 and 2013 to evaluate its fish assemblage structure at seven sites within main- and side-channel habitats where large-scale habitat rehabilitation was undertaken. Understanding the current patterns of fish assemblage structure and their relationships with habitat is important for evaluating the effects of past and future rehabilitation projects on the river. Species-specific habitat associations were modeled, and the variables that best explained the occurrence and relative abundance of fish were identified in order to guide future habitat rehabilitation so that it benefits native species. The results indicated that the side-channel habitats supported higher species richness than the main-channel habitats and that nonnative fishes were closely associated with newly rehabilitated habitats. This research provides valuable insight on the current fish assemblages in the Kootenai River and the assemblage-level responses that may occur as a result of future rehabilitation activities.

Idaho↗

USGS2017

Using variance structure to quantify responses to perturbation in fish catches

We present a case study evaluation of gill-net catches of Walleye Sander vitreus to assess potential effects of large-scale changes in Oneida Lake, New York, including the disruption of trophic interactions by double-crested cormorants Phalacrocorax auritus and invasive dreissenid mussels. We used the empirical long-term gill-net time series and a negative binomial linear mixed model to partition the variability in catches into spatial and coherent temporal variance components, hypothesizing that variance partitioning can help quantify spatiotemporal variability and determine whether variance structure differs before and after large-scale perturbations. We found that the mean catch and the total variability of catches decreased following perturbation but that not all sampling locations responded in a consistent manner. There was also evidence of some spatial homogenization concurrent with a restructuring of the relative productivity of individual sites. Specifically, offshore sites generally became more productive following the estimated break point in the gill-net time series. These results provide support for the idea that variance structure is responsive to large-scale perturbations; therefore, variance components have potential utility as statistical indicators of response to a changing environment more broadly. The modeling approach described herein is flexible and would be transferable to other systems and metrics. For example, variance partitioning could be used to examine responses to alternative management regimes, to compare variability across physiographic regions, and to describe differences among climate zones. Understanding how individual variance components respond to perturbation may yield finer-scale insights into ecological shifts than focusing on patterns in the mean responses or total variability alone.

Transactions of the American Fisheries Society↗

USGS2010

Structure and metamorphism of the Franciscan Complex, Mt. Hamilton area, Northern California

Truncation of metamorphic isograds and fold axes within coherent terranes of Franciscan metagraywacke by intervening zones of melange indicate that the melange is tectonic and formed after the subduction-related metamorphism and folding. These relations are expressed in two terranes of blueschist-facies rocks of the Franciscan Complex in the Mt. Hamilton area, northern California-the Jurassic Yolla Bolly terrane and the structurally underlying Cretaceous Burnt Hills terrane. Local preservation in both terranes of basal radiolarian chert and oceanic basalt beneath continent-derived metagraywacke and argillite demonstrates thrust repetition within the coherent terranes, although these relations are scarce near Mt. Hamilton. The metagraywackes range from albite-pumpellyite blueschists to those containing well-crystallized jadeitic pyroxene, and a jadeite-in isograd can be defined in parts of the area. Primary bedding defines locally coherent structural orientations and folds within the metagraywacke units. These units are crosscut by thin zones of tectonic melange containing blocks of high-grade blueschist, serpentinite, and other exotic rocks, and a broader, but otherwise identical melange zone marks the discordant boundary between the two terranes.

California↗

USGS2010

Prospects for quantifying structure, floristic composition and species richness of tropical forests

Airborne spectral and light detection and ranging (lidar) sensors have been used to quantify biophysical characteristics of tropical forests. Lidar sensors have provided high-resolution data on forest height, canopy topography, volume, and gap size; and provided estimates on number of strata in a forest, successional status of forests, and above-ground biomass. Spectral sensors have provided data on vegetation types, foliar biochemistry content of forest canopies, tree and canopy phenology, and spectral signatures for selected tree species. A number of advances are theoretically possible with individual and combined spectral and lidar sensors for the study of forest structure, floristic composition and species richness. Delineating individual canopies of over-storey trees with small footprint lidar and discrimination of tree architectural types with waveform distributions is possible and would provide scientists with a new method to study tropical forest structure. Combined spectral and lidar data can be used to identify selected tree species and identify the successional status of tropical forest fragments in order to rank forest patches by levels of species richness. It should be possible in the near future to quantify selected patterns of tropical forests at a higher resolution than can currently be undertaken in the field or from space.

International Journal of Remote Sensing↗

USGS2014

Performance of a surface bypass structure to enhance juvenile steelhead passage and survival at Lower Granite Dam, Washington

An integral part of efforts to recover stocks of Pacific salmon Oncorhynchus spp. and steelhead O. mykiss in Pacific Northwest rivers is to increase passage efficacy and survival of juveniles past hydroelectric dams. As part of this effort, we evaluated the efficacy of a prototype surface bypass structure, the removable spillway weir (RSW), installed in a spillbay at Lower Granite Dam, Washington, on the Snake River during 2002, 2003, 2005, and 2006. Radio-tagged juvenile steelhead were released upstream from the dam and their route of passage through the turbines, juvenile bypass, spillway, or RSW was recorded. The RSW was operated in an on-or-off condition and passed 3–13% of the total discharge at the dam when it was on. Poisson rate models were fit to the passage counts of hatchery- and natural-origin juvenile steelhead to predict the probability of fish passing the dam. Main-effect predictor variables were RSW operation, diel period, day of the year, proportion of flow passed by the spillway, and total discharge at the dam. The combined fish passage through the RSW and spillway was 55–85% during the day and 37–61% during the night. The proportion of steelhead passing through nonturbine routes was <88% when the RSW was off during the day and increased to >95% when the RSW was on during the day. The ratio of the proportion of steelhead passed to the proportion of water passing the RSW was from 6.3:1 to 10.0:1 during the day and from 2.7:1 to 5.2:1 during the night. Steelhead passing through the RSW exited the tailrace about 15 min faster than fish passing through the spillway. Mark–recapture single-release survival estimates for steelhead passing the RSW ranged from 0.95 to 1.00. The RSW appeared to be an effective bypass structure compared with other routes of fish passage at the dam.

Idaho, Oregon, Washington↗

USGS2017

Evaluation of genetic population structure of smallmouth bass in the Susquehanna River basin, Pennsylvania

The Smallmouth Bass Micropterus dolomieu was introduced into the Susquehanna River basin, Pennsylvania, nearly 150 years ago. Since introduction, it has become an economically and ecologically important species that supports popular recreational fisheries. It is also one of the most abundant top predators in the system. Currently, there is no information on the level of genetic diversity or genetic structuring that may have occurred since introduction. An understanding of genetic diversity is important for the delineation of management units and investigation of gene flow at various management scales. The goals of this research were to investigate population genetic structure of Smallmouth Bass at sites within the Susquehanna River basin and to assess genetic differentiation relative to Smallmouth Bass at an out-of-basin site (Allegheny River, Pennsylvania) located within the species’ native range. During spring 2015, fin clips ( n = 1,034) were collected from adults at 11 river sites and 13 tributary sites in the Susquehanna River basin and at one site on the Allegheny River. Fin clips were genotyped at 12 polymorphic microsatellite loci. Based on our results, adults sampled throughout the Susquehanna River basin did not represent separate genetic populations. There were only subtle differences in genetic diversity among sites (mean pairwise genetic differentiation index F ST = 0.012), and there was an overall lack of population differentiation ( K = 3 admixed populations). The greatest genetic differentiation was observed between fish collected from the out-of-basin site and those from the Susquehanna River basin sites. Knowledge that separate genetic populations of Smallmouth Bass do not exist in the Susquehanna River basin is valuable information for fisheries management in addition to providing baseline genetic data on an introduced sport fish population.

Pennsylvania↗

USGS2019

Potential shifts in zooplankton community structure in response to changing ice regimes and hydrologic connectivity

Changing Arctic climate may alter freshwater ecosystems as a result of warmer surface waters, longer open-water periods, reduced wintertime lake ice growth, and altered hydrologic connectivity. This study aims to characterize zooplankton community composition and size structure in the context of hydrologic connectivity and ice regimes in Arctic lakes. Between 2011 and 2016, we sampled the phytoplankton, zooplankton, and fish communities from a set of representative lakes on the Arctic Coastal Plain (ACP) of northern Alaska to determine potential food web responses to changing Arctic ecosystems. Multivariate analyses showed that time from ice-out had a strong influence on zooplankton community structure and that seasonal succession of zooplankton differed between lakes with varying hydrologic connectivity. Trends were observed suggesting that large-bodied zooplankton ( Daphnia , calanoid copepods) may be more prevalent in poorly connected lakes with low fish diversity. Large-bodied zooplankton displayed higher biomass in lakes with high occurrences of bedfast ice, while small-bodied zooplankton ( Bosmina , rotifers) displayed highest biomass in deeper lakes with low occurrences of bedfast ice. Our results contribute to limited knowledge of zooplankton in remote lakes of the ACP and suggest that the anticipated changes to aquatic ecosystems in the Arctic may include energetically less efficient plankton food webs.

Alaska↗

USGS1997

A structural equation model of plant species richness and its application to a coastal wetland

Studies of plant species richness have often emphasized the role of either community biomass (as an indicator of density effects) or abiotic factors. In this article we present a general model that simultaneously examines the relative importance of abiotic and density effects. General and specific models were developed to examine the importance of abiotic conditions, disturbance, and community biomass on plant species richness. Models were evaluated using structural equation modeling based on data from 190 plots across a coastal marsh landscape. The accepted model was found to explain 45% of the observed variation in richness, 75% of biomass, and 65% of light penetration. Model results indicate that abiotic conditions have both direct effects on the species pool and indirect effects on richness mediated through effects on biomass and shading. Effects of disturbance were found to be indirect via biomass. Strong density effects on richness were indicated by the results, and canopy light penetration was found to be a better predictor of richness than was biomass. Overall, it appears that richness in this coastal landscape is controlled in roughly equal proportions by abiotic influences on the species pool and density effects, with disturbance playing a lesser role. The structure of the general model presented should be applicable to a wide variety of herbaceous plant communities.

Louisiana, Mississippi↗

USGS2002

Composition of cavity-nesting bird communities in montane aspen woodland fragments: The roles of landscape context and forest structure

We compared cavity-nesting bird communities in aspen ( Populus tremuloides ) woodland fragments classified on the basis of vegetation structure (tree density) and landscape context (surrounding vegetation). We found very few cavity nesters in fragments predominantly surrounded by forests. Fragments adjacent to meadows contained more species and a greater abundance of cavity nesters. Species richness and abundance were higher in sparsely than in densely treed meadow fragments. Because secondary cavity nesters are often limited by cavity availability, we augmented natural cavities with nest boxes. Although only five boxes contained bird nests, these were all in sparse aspen fragments predominantly surrounded by meadows. However, we found 25 northern flying squirrel ( Glaucomys sabrinus ) nests in boxes, none of which were in sparse meadow fragments. In addition to high-lighting the importance of landscape context in avian and mammalian habitat relationships, our results suggest that predator or competitor interactions may help structure this cavity-nester community.

Utah↗

USGS2017

Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements

The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldarius genomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobus species result in the relatively low diversity of the S. acidocaldarius genome.

Genome Biology and Evolution↗

USGS2020

Quantifying model structural uncertainty using airborne electromagnetic data

The ability to quantify structural uncertainty in geological models that incorporate geophysical data is affected by two primary sources of uncertainty: geophysical parameter uncertainty and uncertainty in the relationship between geophysical parameters and geological properties of interest. Here, we introduce an open-source, trans-dimensional Bayesian Markov chain Monte Carlo (McMC) algorithm GeoBIPy—Geophysical Bayesian Inference in Python—for robust uncertainty analysis of time-domain or frequency-domain airborne electromagnetic (AEM) data. The McMC algorithm provides a robust assessment of geophysical parameter uncertainty using a trans-dimensional approach that lets the AEM data inform the level of model complexity necessary by allowing the number of model layers itself to be an unknown parameter. Additional components of the Bayesian algorithm allow the user to solve for parameters such as data errors or corrections to the measured instrument height above ground. Probability distributions for a user-specified number of lithologic classes are developed through posterior clustering of McMC-derived resistivity models. Estimates of geological model structural uncertainty are thus obtained through the joint probability of geophysical parameter uncertainty and the uncertainty in the definition of each class. Examples of the implementation of this algorithm are presented for both time-domain and frequency-domain AEM data acquired in Nebraska, USA.

Nebraska↗

USGS2019

Micro-geographic population genetic structure within Arctic cod (Boreogadus saida) in Beaufort Sea of Alaska

Many marine organisms show significant levels of genetic heterogeneity on local spatial scales despite exhibiting limited genetic structure at large geographic scales which can be produced through a variety of mechanisms. The Arctic cod ( Boreogadus saida ) is a circumpolar species and is a vital species in Arctic food webs. To examine population genetic structure of Arctic cod at macro- and micro-geographic scales, we characterized variation at mitochondrial DNA (mtDNA) and microsatellite loci among Arctic cod located in the Chukchi and Beaufort seas in Alaska. We found two distinct mtDNA haplotype clusters, although there was no underlying geographic pattern ( F ST = −0.001). Congruent with this finding, microsatellite loci suggested a panmictic population ( F ST = 0.001) across northern Alaskan marine waters at a large spatial scale. However, we found slight but significant micro-geographic partitioning of genetic variation in the southern shelf of the Beaufort Sea that appeared to be associated with the western reaches of the Mackenzie River plume. This fine-scale spatial pattern was not associated with kin-associated groups, suggesting larvae cohorts are not remaining together throughout development. We hypothesize that this pattern reflects the intermixing of Pacific and Arctic origin lineages of Arctic cod.

Alaska↗

USGS2026

Cnidarian–algal partnerships structure bacterial communities during strobilation in Cassiopea xamachana

Cnidarian–algal (Symbiodiniaceae) symbioses rely on complex interactions among the cnidarian host, algal symbionts, and associated bacterial communities. In the upside-down jellyfish Cassiopea xamachana , the polyp-to-medusa transition (strobilation) requires the establishment of symbiosis with Symbiodiniaceae algal partners, yet bacterial community dynamics during this developmental process remain unknown. Here, we experimentally induced symbiosis in aposymbiotic polyps using four algal treatments: xenic Symbiodinium microadriaticum (native symbiont), xenic Breviolum minutum , antibiotic-treated B. minutum , and a photosynthetically impaired B. minutum mutant. We combined 16S rRNA gene sequencing with measurements of photosynthetic efficiency, asexual budding, and algal surface N-glycan profiles to characterize holobiont assembly during symbiosis onset and strobilation. Algal treatment structured bacterial communities in both algal cultures and polyp tissues. Our analyses identified a set of amplicon sequence variants that consistently distinguished strobilating polyps from non-strobilating aposymbiotic and mutant polyps, in addition to potential bacterial biomarkers associated with successful metamorphosis. Strobilation was associated with the enrichment of bacterial communities putatively involved in sulfur and nitrogen cycling, whereas non-strobilating aposymbiotic and mutant polyps were characterized by opportunistic bacteria and increased community variability. Together, these results reveal coordinated changes in algal physiology, surface glycan profiles, and bacterial community structure associated with successful strobilation in C. xamachana and support a model in which tripartite host–alga–bacteria interactions influence cnidarian life stage transitions.

ISME Communications↗

USGS2012

Variation in migratory behavior influences regional genetic diversity and structure among American kestrel populations (Falco sparverius) in North America

Birds employ numerous strategies to cope with seasonal fluctuations in high-quality habitat availability. Long distance migration is a common tactic; however, partial migration is especially common among broadly distributed species. Under partial migration systems, a portion of a species migrates, whereas the remainder inhabits breeding grounds year round. In this study, we identified effects of migratory behavior variation on genetic structure and diversity of American Kestrels (Falco sparverius), a widespread partial migrant in North America. American Kestrels generally migrate; however, a resident group inhabits the southeastern United States year round. The southeastern group is designated as a separate subspecies (F. s. paulus) from the migratory group (F. s. sparverius). Using mitochondrial DNA and microsatellites from 183 and 211 individuals, respectively, we illustrate that genetic structure is stronger among nonmigratory populations, with differentiation measures ranging from 0.060 to 0.189 depending on genetic marker and analysis approach. In contrast, measures from western North American populations ranged from 0 to 0.032. These findings suggest that seasonal migratory behavior is also associated with natal and breeding dispersal tendencies. We likewise detected significantly lower genetic diversity within nonmigratory populations, reflecting the greater influence of genetic drift in small populations. We identified the signal of population expansion among nonmigratory populations, consistent with the recent establishment of higher latitude breeding locations following Pleistocene glacial retreat. Differentiation of F. s. paulus and F. s. sparverius reflected subtle differences in allele frequencies. Because migratory behavior can evolve quickly, our analyses suggest recent origins of migratory American Kestrel populations in North America.

Journal of Heredity↗