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At least 181 records · Page 10Linked to original sources

USGS1989

Tectono-stratigraphic evolution of the Early Proterozoic Wisconsin magmatic terranes of the Penokean Orogen

The Early Proterozoic Penokean Orogen developed along the southern margin of the Archean Superior craton. The orogen consists of a northern deformed continental margin prism overlying an Archean basement and a southern assemblage of oceanic arcs, the Wisconsin magmatic terranes. The south-dipping Niagara fault (suture) zone separates the south-facing continental margin from the accreted arc terranes. The suture zone contains a dismembered ophiolite.The Wisconsin magmatic terranes consist of two terranes that are distinguished on the basis of lithology and structure. The northern Pembine–Wausau terrane contains a major succession of tholeiitic and calc-alkaline volcanic rocks deposited in the interval 1860–1889 Ma and a more restricted succession of calc-alkaline volcanic rocks deposited about 1835 – 1845 Ma. Granitoid rocks ranging in age from about 1870 to 1760 Ma intrude the volcanic rocks. The older succession was generated as island arcs and (or) closed back-arc basins above the south-dipping subduction zone (Niagara fault zone), whereas the younger one developed as island arcs above a north-dipping subduction zone, the Eau Pleine shear zone. The northward subduction followed deformation related to arc–continent collision at the Niagara suture at about 1860 Ma. The southern Marshfield terrane contains remnants of mafic to felsic volcanic rocks about 1860 Ma that were deposited on Archean gneiss basement, foliated tonalite to granite bodies ranging in age from about 1890 to 1870 Ma, and younger undated granite plutons. Following amalgamation of the two arc terranes along the Eau Pleine suture at about 1840 Ma, intraplate magmatism (1835 Ma) produced rhyolite and anorogenic alkali-feldspar granite that straddled the internal suture.

Wisconsin↗

USGS2020

Integrating broad‐scale data to assess demographic and climatic contributions to population change in a declining songbird

Climate variation and trends affect species distribution and abundance across large spatial extents. However, most studies that predict species response to climate are implemented at small spatial scales or are based on occurrence‐environment relationships that lack mechanistic detail. Here, we develop an integrated population model (IPM) for multi‐site count and capture‐recapture data for a declining migratory songbird, Wilson's warbler ( Cardellina pusilla ), in three genetically distinct breeding populations in western North America. We include climate covariates of vital rates, including spring temperatures on the breeding grounds, drought on the wintering range in northwest Mexico, and wind conditions during spring migration. Spring temperatures were positively related to productivity in Sierra Nevada and Pacific Northwest genetic groups, and annual changes in productivity were important predictors of changes in growth rate in these populations. Drought condition on the wintering grounds was a strong predictor of adult survival for coastal California and Sierra Nevada populations; however, adult survival played a relatively minor role in explaining annual variation in population change. A latent parameter representing a mixture of first‐year survival and immigration was the largest contributor to variation in population change; however, this parameter was estimated imprecisely, and its importance likely reflects, in part, differences in spatio‐temporal distribution of samples between count and capture‐recapture data sets. Our modeling approach represents a novel and flexible framework for linking broad‐scale multi‐site monitoring data sets. Our results highlight both the potential of the approach for extension to additional species and systems, as well as needs for additional data and/or model development.

Ecology and Evolution↗

USGS1999

[Book review] Cowbirds and Other Brood Parasites by Catherine Ortega. Tucson, Arizona: University of Arizona Press (1998). The Avian Brood Parasites: Deception at the Nest by Paul A. Johnsgard. New York: Oxford University Press (1997) Parasitic Birds and their Hosts: Studies in Coevolution edited by S.I. Rothstein & S.K. Robinson. New York: Oxford University Press (1998)

We are in a golden age for the study of brood parasitism, judging from both the quantity and quality of recent scientific publications on cuckoos, cowbirds and parasitic finches by investigators working in Europe, the Americas, Africa and Asia. As Johnsgard (1997) remarks in his preface, the evolutionary, ecological, and behavioural questions posed by obligate brood parasites are among the most intriguing contemporary ornithological topics. Rothstein & Robinson (1998) explain that brood parasites make ideal subjects for testing the generality of models for the evolution of social and mating behaviour, foraging behaviour, spatial distribution, and vocal development, because the strategy of providing no parental care removes constraints imposed on other birds. Since Aristotle, people have been fascinated by brood parasites, but only in the past two decades has the number of investigators working on this topic reached a critical mass and created momentum that promises many breakthroughs. New studies are being completed so rapidly that a general book is inevitably out of date on some topics by the time it is published. A complete library on brood parasitism should add two recent volumes (Morrison et al. 1999; Smith et al., in press).to the three reviewed here.

Animal Behaviour↗

USGS2014

Lake trout in northern Lake Huron spawn on submerged drumlins

Recent observations of spawning lake trout Salvelinus namaycush near Drummond Island in northern Lake Huron indicate that lake trout use drumlins, landforms created in subglacial environments by the action of ice sheets, as a primary spawning habitat. From these observations, we generated a hypothesis that may in part explain locations chosen by lake trout for spawning. Most salmonines spawn in streams where they rely on streamflows to sort and clean sediments to create good spawning habitat. Flows sufficient to sort larger sediment sizes are generally lacking in lakes, but some glacial bedforms contain large pockets of sorted sediments that can provide the interstitial spaces necessary for lake trout egg incubation, particularly if these bedforms are situated such that lake currents can penetrate these sediments. We hypothesize that sediment inclusions from glacial scavenging and sediment sorting that occurred during the creation of bedforms such as drumlins, end moraines, and eskers create suitable conditions for lake trout egg incubation, particularly where these bedforms interact with lake currents to remove fine sediments. Further, these bedforms may provide high-quality lake trout spawning habitat at many locations in the Great Lakes and may be especially important along the southern edge of the range of the species. A better understanding of the role of glacially-derived bedforms in the creation of lake trout spawning habitat may help develop powerful predictors of lake trout spawning locations, provide insight into the evolution of unique spawning behaviors by lake trout, and aid in lake trout restoration in the Great Lakes.

Michigan↗

USGS2009

A selection and archiving strategy for science records

The U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center archives electronic science collections that total over two petabytes in size and over 100,000 rolls of aerial and satellite film. Limited resources, the evolution of missions, and recommendations from advisory committees have led to the development of a scientific records appraisal process as a means for determining long-term archiving priorities. The process was formed through extensive literature searches describing approaches used to appraise administrative, physical artifacts, and science records. Less information was available that specifically addressed science records; therefore, relevant portions from each records appraisal process was assembled. In addition, involvement with the appropriate stakeholders was deemed critical and led to the active participation of scientists, records managers, and senior managers in the process. As part of the documentation portion of the process, an extensive online tool was developed to capture information describing each collection and detail preservation or access challenges that may be part of a collection. The U.S. National Archives and Records Administration recommends the tool as a best practice for U.S. federal agencies. To date, over 30 science collections have been appraised. This paper will detail the process used to appraise science collections for long-term archiving, the composition and rationale for the tool elements, and the results the USGS has attained.

Conference Paper↗

USGS2015

Sample descriptions and geophysical logs for cored well BP-3-USGS, Great Sand Dunes National Park and Preserve, Alamosa County, Colorado

The BP-3-USGS well was drilled at the southwestern corner of Great Sand Dunes National Park in the San Luis Valley, south-central Colorado, 68 feet (ft, 20.7 meters [m]) southwest of the National Park Service’s boundary-piezometer (BP) well 3. BP-3-USGS is located at latitude 37°43ʹ18.06ʺN. and longitude 105°43ʹ39.30ʺW., at an elevation of 7,549 ft (2,301 m). The well was drilled through poorly consolidated sediments to a depth of 326 ft (99.4 m) in September 2009. Water began flowing from the well after penetrating a clay-rich layer that was first intercepted at a depth of 119 ft (36.3 m). The base of this layer, at an elevation of 7,415 ft (2,260 m) above sea level, likely marks the top of a regional confined aquifer recognized throughout much of the San Luis Valley. Approximately 69 ft (21 m) of core was recovered (about 21 percent), almost exclusively from clay-rich zones. Coarser grained fractions were collected from mud extruded from the core barrel or captured from upwelling drilling fluids. Natural gamma-ray, full waveform sonic, density, neutron, resistivity, spontaneous potential, and induction logs were acquired. The well is now plugged and abandoned. This report presents lithologic descriptions from the well samples and core, along with a compilation and basic data processing of the geophysical logs. The succession of sediments in the well can be generalized into three lithologic packages: (1) mostly sand from the surface to about 77 ft (23.5 m) depth; (2) interbedded sand, silt, and clay, decreasing in overall grain size downward, from 77 to 232 ft (23.5 to 70.7 m) depth; and (3) layers of massive clay alternating with layers of fine sand to silt from 232 to 326 ft (70.7 to 99.4 m), the total depth of the well. The topmost clay layers of the deepest package have a blue tint, prompting a correlation with the “blue clay” of the San Luis Valley that is commonly considered as the top of the confined aquifer. However, a confining clay was intercepted 113 ft (34.4 m) higher than the blue clay in BP-3-USGS. Most of the geophysical logs have good correspondence to the lithologic variations in the well. Exceptions are the gamma-ray log, which is likely affected by naturally occurring radiation from abundant volcanic detritus, and one interval within the deepest lithologic package, which appears to be abnormally electrically conductive. Resistivity logs and variations in sand versus clay content within the well are consistent with electrical resistivity models derived from time-domain electromagnetic geophysical surveys for the area. In particular, the topmost blue clay corresponds to a strong electrical conductor that is prominent in the electromagnetic geophysical data throughout the park and vicinity. BP-3-USGS was sited to test hypotheses developed from geophysical studies and to answer questions about the history and evolution of Pliocene and Pleistocene Lake Alamosa, which is represented by lacustrine deposits sampled by the well. The findings reported here represent a basis from which future studies can answer these questions and address other important scientific questions in the San Luis Valley regarding geologic history and climate change, groundwater hydrology, and geophysical interpretation.

Colorado↗

USGS2002

Map Showing Seacliff Response to Climatic and Seismic Events, Seabright Beach, Santa Cruz County, California

Introduction The coastal cliffs along much of the central California coast are actively retreating. Large storms and periodic earthquakes are responsible for most of the documented sea cliff slope failures. Long-term average erosion rates calculated for this section of coast do not provide the spatial or temporal data resolution necessary to identify the processes responsible for retreat of the sea cliffs where episodic retreat threatens homes and community infrastructure. Research suggests that more erosion occurs along the California coast over a short time scale, during periods of severe storms or seismic activity, than occurs during decades of normal weather or seismic quiescence. This is the third map in a series of maps prepared to document the processes of short-term sea cliff retreat through the identification of slope failure styles, spatial variability of failures, and temporal variation in retreat amounts in an area that has been identified as an erosion hotspot. This map presents sea cliff failure and retreat data from the Seabright Beach section, California, which is located on the east side of Santa Cruz along the northern Monterey Bay coast. The data presented in this map series provide high-resolution spatial and temporal information on the location, amount, and processes of sea cliff retreat in Santa Cruz, California. These data show the response of the sea cliffs to both large magnitude earthquakes and severe climatic events such as El Ni?os; this information may prove useful in predicting the future response of the cliffs to events of similar magnitude. The map data can also be incorporated into Global Information System (GIS) for use by researchers and community planners. During this study we developed a method for investigating short-term processes of sea cliff evolution using rectified photographic stereo models. This method allows us to document the linear extent of cliff failures, the spatial and temporal relationship between failures, and the type or style of slope failure. Seabright Beach extends 0.9 km from San Lorenzo Point on the west to the Santa Cruz Yacht Harbor on the east. The cliffs at Seabright Beach are completely protected from wave attack by a wide beach. The protective beach is a relatively recent feature that formed after the emplacement of the Santa Cruz Yacht Harbor jetty in 1963-1964. Prior to the completion of the jetty, the cliffs at Seabright Beach were subject to daily wave attack. The data in this study are post-jetty construction; therefore, the sea cliff failures and cliff retreat are the result of nonmarine processes (rainfall, groundwater and seismic shaking). The 8 to 15 m high cliffs at Seabright Beach are composed of the Miocene to Pliocene Purisima Formation, which is overlain by unconsolidated Pleistocene terrace deposits. The relative thickness of these units varies along the length of the cliff. At the west end of Seabright Beach, including San Lorenzo Point, nearly the entire cliff section is composed of Purisima Formation and is capped by less than 2 m of terrace deposits. In this exposure, the Purisima Formation is a moderately weathered, moderately indurated massive sandstone. The height of the cliffs and the thickness of the Purisima Formation decrease to the east. In the cliffs immediately adjacent to the harbor, the entire exposure is composed of terrace deposits. Toe-slope debris and wind-blown sand form a nearly continuous fan along the cliff base that obscure the lower portion of the cliff. This study documents the impacts of earthquakes and large storms to the sea cliffs in the Seabright Beach section. The first event is the 1989 Loma Prieta earthquake, a M7.1 earthquake that caused widespread damage to the area stretching from Santa Cruz to the San Francisco Bay. The epicenter of the earthquake was located in the Santa Cruz Mountains, approximately 9 km inland from the coast. Extensive block and debris falls, induced by the seismic shaking, occ

Miscellaneous Field Studies Map↗

USGS1989

Selected water-quality characteristics and flow of ground water in the San Luis basin, including the Conejos River subbasin, Colorado and New Mexico

Chemical analyses of water from 99 wells and 19 springs in the San Luis basin in Colorado and New Mexico were evaluated to determine selected water quality characteristics as an aid in understanding the flow of groundwater in the basin. The evaluation shows that the distribution of chemical water types in the basin is consistent with chemical changes to be expected along flow paths in rocks typical of those in the basin. The San Luis basin area is underlain by a surficial (< 100-ft-thick) unconfined aquifer and, in turn, by a confining bed and a deeper confined aquifer. Previous studies have indicated that the groundwater system is recharged around the edges of the basin and that groundwater then moves toward discharge areas in the topographically closed part of the basin and along principal streams. The evaluation of water quality data showed that groundwater at the perimeter of the San Luis basin is primarily a calcium bicarbonate type, which is typical in recharge areas. Groundwater near the center of the basin is primarily a sodium bicarbonate type, which is typical of groundwater in downgradient areas. The change in principal cation from calcium to sodium indicates chemical evolution of the water along the groundwater flow path and supports previously developed concepts of groundwater movement in the basin. The exchange of calcium for sodium along the flow path also is assumed to occur in the Conejos River subbasin. Upgradient wells yield calcium bicarbonate type water, whereas downgradient wells yield sodium bicarbonate type water. However, an exception to this relation is found at McIntire Spring, which yields calcium bicarbonate type water from a downgradient location. The source of water discharging from the spring may be the confined aquifer, with hydraulic connection along the Manassa fault. The concentration of dissolved solids in water from both the unconfined and confined aquifers increases downgradient. The increase is dramatic in the closed basin, ranging from < 500 mg/L to > 30 ,000 mg/L. In this area, the normal increase in concentration by dissolution of minerals along the flow path is exceeded by the increase due to evapotranspiration from the shallow water table. (Lantz-PTT)

Water-Resources Investigations Report↗

USGS1997

Bulk-friction modeling of afterslip and the modified Omori law

Afterslip data from the Superstition Hills fault in southern California, a creep event on the same fault, the modified Omori law, and cumulative moments from aftershocks of the 1957 Aleutian Islands earthquake all indicate that the original formulation by Dieterich (1981) [Constitutive properties of faults with simulated gouge. AGU, Geophys. Monogr. 24, 103–120] for friction evolution is more appropriate for systems far from instability than the commonly used approximation developed by Ruina (1983) [Slip instability and state variable friction laws. J. Geophys. Res. 88, 10359–10370] to study instability. The mathematical framework we use to test the friction models is a one-dimensional, massless spring-slider under the simplifying assumption, proposed by Scholz (1990) [The Mechanics of Earthquakes and Faulting. Cambridge University Press] and used by Marone et al. (1991) [On the mechanics of earthquake afterslip. J. Geophys. Res., 96: 8441–8452], that the state variable takes on its velocity-dependent steady-state value throughout motion in response to a step in stress. This assumption removes explicit state-variable dependence from the model, obviating the need to consider state-variable evolution equations. Anti-derivatives of the modified Omori law fit our data very well and are very good approximate solutions to our model equations. A plausible friction model with Omori-law solutions used by Wesson (1988) [Dynamics of fault creep. J. Geophys. Res. 93, 8929–8951] to model fault creep and generalized by Rice (1983) [Constitutive relations for fault slip and earthquake instabilities. Pure Appl. Geophys. 121, 443–475] to a rate-and-state variable friction model yields exactly Omori's law with exponents greater than 1, but yields unstable solutions for Omori exponents less than 1. We estimate from the Dieterich formulation the dimensionless parameter a∗ which is equal to the product of the nominal coefficient of friction and the more commonly reported friction parameter a . We find that a∗ is typically positive, qualitatively consistent with laboratory observations, although our observations are considerably larger than laboratory values. However, we also find good model fits for a∗ < 0 when data correspond to Omori exponents less than 1. A modification of the stability analysis by Rice and Ruina (1983) [Stability of steady frictional slipping. J. Appl. Mech. 50, 343–349] indicates that a∗ < 0 is not a consequence of our assumption regarding state-variable evolution. A consistent interpretation of a∗ < 0 in terms of laboratory models appears to be that the data are from later portions of processes better characterized by two-state-variable friction models. a∗ < 0 is explained by assuming that our data cannot resolve the co-seismic evolution of a short-length-scale state variable to a velocity-weakening state; our parameterization leads to an apparent negative instantaneous viscosity. We estimate the largest critical slip distance associated with afterslip to be ∼1–10 cm, consistent with other estimates for near-surface materials. We assume that our observed large values for a∗ reflect the fact that our model ignores the geometrical complexities of three-dimensional stresses in fractured crustal materials around a fault zone with frictional stresses that vary on a fault surface. Our one-dimensional model parameters reflect spatially averaged, bulk , stress and frictional properties of a fault zone, where we clearly cannot specify the details of the averaging process. Our analysis of Omori's law suggests that bulk-frictional properties of a fault zone are well described by our simple laboratory-based models, but they would need to change during the seismic cycle for a mainshock instability to recur, unless a mainshock-aftershock sequence were characterized by a process similar to the arrested instabilities possible in two-state-variable systems.

Tectonophysics↗

USGS2017

Evolution of strain localization in variable-width three-dimensional unsaturated laboratory-scale cut slopes

To experimentally validate a recently developed theory for predicting the stability of cut slopes under unsaturated conditions, the authors measured increasing strain localization in unsaturated slope cuts prior to abrupt failure. Cut slope width and moisture content were controlled and varied in a laboratory, and a sliding door that extended the height of the free face of the slope was lowered until the cut slope failed. A particle image velocimetry tool was used to quantify soil displacement in the x - y "> x - y (horizontal) and x - z "> x -z (vertical) planes, and strain was calculated from the displacement. Areas of maximum strain localization prior to failure were shown to coincide with the location of the eventual failure plane. Experimental failure heights agreed with the recently developed stability theory for unsaturated cut slopes (within 14.3% relative error) for a range of saturation and cut slope widths. A theoretical threshold for sidewall influence on cut slope failures was also proposed to quantify the relationship between normalized sidewall width and critical height. The proposed relationship was consistent with the cut slope experiment results, and is intended for consideration in future geotechnical experiment design. The experimental data of evolution of strain localization presented herein provide a physical basis from which future numerical models of strain localization can be validated.

Journal of Engineering Mechanics↗

USGS2014

Contrasting volcanism in Hawaiʻi and the Galápagos

The archipelagos of Hawai‘i and the Galápagos originated at mantle hotspots, yet the volcanoes that make up the island chains differ in most respects. Some of the most important differences include the dynamics of magma supply, characteristics of magma storage and transport, morphology, and compositional and structural evolution. Of particular significance in the Galápagos is the lack of well-developed rift zones, which may be related to higher rates of pre-eruptive inflation compared to Hawai‘i, and the absence of widespread flank instability—a common feature of Hawai‘i's volcanoes. The close proximity of the Galápagos to a mid-ocean-ridge system may account for many of the differences between Hawaiian and Galápagos volcanoes. The Galápagos archipelago is built on young, thin oceanic crust, which might allow for contemporaneous growth of numerous volcanoes, and its volcanoes are fed by a mix of plume and asthenospheric melt sources. Hawaiian volcanoes, in contrast, grew in the middle of the Pacific Plate on older, thicker crust, where localized changes in mantle and lithosphere structure and composition did not exert dominant control over volcano evolution.

Book chapter↗

USGS2006

Evolution of a Holocene delta driven by episodic sediment delivery and coseismic deformation, Puget Sound, Washington, USA

Episodic, large-volume pulses of volcaniclastic sediment and coseismic subsidence of the coast have influenced the development of a late Holocene delta at southern Puget Sound. Multibeam bathymetry, ground-penetrating radar (GPR) and vibracores were used to investigate the morphologic and stratigraphic evolution of the Nisqually River delta. Two fluvial–deltaic facies are recognized on the basis of GPR data and sedimentary characteristics in cores, which suggest partial emplacement from sediment-rich floods that originated on Mount Rainier. Facies S consists of stacked, sheet-like deposits of andesitic sand up to 4 m thick that are continuous across the entire width of the delta. Flat-lying, highly reflective surfaces separate the sand sheets and comprise important facies boundaries. Beds of massive, pumice- and charcoal-rich sand overlie one of the buried surfaces. Organic-rich material from that surface, beneath the massive sand, yielded a radiocarbon age that is time-correlative with a series of known eruptive events that generated lahars in the upper Nisqually River valley. Facies CF consists of linear sandbodies or palaeochannels incised into facies S on the lower delta plain. Radiocarbon ages of wood fragments in the sandy channel-fill deposits also correlate in time to lahar deposits in upstream areas. Intrusive, sand-filled dikes and sills indicate liquefaction caused by post-depositional ground shaking related to earthquakes. Continued progradation of the delta into Puget Sound is currently balanced by tidal-current reworking, which redistributes sediment into large fields of ebb- and flood-oriented bedforms.

Washington↗

USGS2011

Relationships between silicic plutonism and volcanism: Geochemical evidence

Field associations (voluminous ash flow deposits, rhyolitic stocks and dykes, ring complexes), evidence of repeated influxes of mafic magma, and thermal constraints indicate that many high-level silicic plutons (magma chambers) acted as open systems for considerable parts of their history. The long thermal lifetime, as well as other evidence from the volcanic record, suggests that some such systems reached a quasi-steady state in which magma input was balanced by magma output for times longer than those required for crystallisation. Reconstruction of the evolution of large, long-lived caldera-forming systems, such as that of the Jemez Mountains, New Mexico, indicates that many chambers have lost a highly fractionated silicic cap, in some cases cyclically. Crystallised plutons may contain no obvious record of this evolutionary phase. Geochemical data from silicic ash flow deposits can be used to reconstruct the volcanic stage of pluton development. Many silicic systems, especially of alkaline affinity, apparently pass from a stage in which melt evolution is dominated by crystal-liquid processes to one in which other processes may also contribute to differentiation. Apparently, the transition is most readily achieved in volatile-rich, alkaline silicic systems emplaced in complex, ancient sialic crust of the cratons. Once established, the preservation of highly fractionated caps on magma chambers requires a balance between thermal input and cooling-induced crystallisation. If heat enters the system too quickly, the cap may get stirred into the dominant magma volume by convection. If heat input is too slow, the magma body will crystallise inward from the margins, and the plutonic-consolidation stage will begin. © 1988, Royal Society of Edinburgh. All rights reserved.

Transactions of the Royal Society of Edinburgh, Ea↗

USGS2026

Frameworks for assessing tsunami hazard and risk

Tsunamis are multiscale phenomena resulting from a water column displacement that may be induced by multiple sources, and range from local scale inundation processes to ocean-wide scale wave propagation. Different strategies may be required to model tsunami evolution at different scales and to characterize various intensity measures. Research in tsunami hazard and risk has focused mostly on the tsunami effects such as the wave heights or flow depths. This chapter reviews the evolution of tsunami hazard and risk assessment methodologies, with particular emphasis on the development of probabilistic approaches. Building on advances in numerical modeling and uncertainty analysis, two main frameworks for Probabilistic Tsunami Hazard and Risk Analysis (PTHA/PTRA) are described. Framework 1 (FW1) focuses on quantitative methods, including fully simulation-based assessments (FW1A), integration of hazard with vulnerability and loss models (FW1B), consideration of dynamic processes such as tidal and sea-level variations (FW1C), and approaches using limited scenario sets (FW1D). Framework 2 (FW2) complements this by incorporating indicator-based vulnerability assessments, both physical (FW2A) and social, multi-dimensional (FW2B).

Book chapter↗

USGS2023

Environmental antimicrobial resistance gene detection from wild bird habitats using two methods: A commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole-genome sequencing

Objectives A variety of methods have been developed to detect antimicrobial resistance (AMR) in different environments to better understand the evolution and dissemination of this public health threat. Comparisons of results generated using different AMR detection methods, such as quantitative PCR (qPCR) and whole-genome sequencing (WGS), are often imperfect, and few studies have analysed samples in parallel to evaluate differences. In this study, we compared bacterial culture and WGS to a culture-independent commercially available qPCR assay to evaluate the concordance between methods and the utility of each in answering research questions regarding the presence and epidemiology of AMR in wild bird habitats. Methods We first assessed AMR gene detection using qPCR in 45 bacterial isolates from which we had existing WGS data. We then analysed 52 wild bird faecal samples and 9 spatiotemporally collected water samples using culture-independent qPCR and WGS of phenotypically resistant indicator bacterial isolates. Results Overall concordance was strong between qPCR and WGS of bacterial isolates, although concordance differed among antibiotic classes. Analysis of wild bird faecal and water samples revealed that more samples were determined to be positive for AMR via qPCR than via culture and WGS of bacterial isolates, although qPCR did not detect AMR genes in two samples from which phenotypically resistant isolates were found. Conclusions Both qPCR and culture followed by sequencing may be effective approaches for characterising AMR genes harboured by wild birds, although data streams produced using these different tools may have advantages and disadvantages that should be considered given the application and sample matrix.

Journal of Global Antimicrobial Resistance↗

USGS2007

ADCP measurements of gravity currents in the Chicago River, Illinois

A unique set of observations of stratified flow phenomena in the Chicago River was made using an upward-looking acoustic Doppler current profiler (ADCP) during the period November 20, 2003 to February 1, 2004. Water density differences between the Chicago River and its North Branch (NB) seem to be responsible for the development of gravity currents. With the objective of characterizing the occurrence, frequency, and evolution of such currents, the ADCP was configured to continuously collect high-resolution water velocity and echo intensity profiles in the Chicago River at Columbus Drive. During the observation period, 28 gravity current events were identified, lasting a total of 77% of the time. Sixteen of these events were generated by underflows from the NB and 12 of these events were generated by overflows from the NB. On average, the duration of the underflow and overflow events was 52.3 and 42.1 h, respectively. A detailed analysis of one underflow event, which started on January 7, 2004, and lasted about 65h, was performed. This is the first time that ADCP technology has been used to continuously monitor gravity currents in a river. ?? 2007 ASCE.

Journal of Hydraulic Engineering↗

USGS1976

The abundance and diversity of the herpetofaunas of tropical forest litters

Quantitative and qualitative samples of amphibian and lizard faunas were taken from forest litter in Costa Rica and compared with similar samples collected in Borneo, the Philippines, and Panama. Animal abundance is about ten times greater in Costa Rican lowland wet forest than in Borneo. Radically different routes and rates of energy flow are postulated to account for the difference. In a series of upland (1010-1425 m) samples in the Philippines, the number of litter lizards and frogs increases with elevation. A single upland (1200 m) Costa Rican sample contains about three times as many animals per 100 m2 as two lowland sites. This increase with altitude correlates well with hypotheses that overall tropical forest productivity is greatest at intermediate elevations. Herpetofaunal densities are greater in wet areas compared to dry sites and flat terrain compared to slopes. These observations are linked to the greater variation and lesser total litter fall in dry sites and/or slopes. The number of species of amphibians and lizards regularly inhabiting the litter is similar in all wet lowland forests studied. Increasing elevation and decreasing rainfall correlate with faunas having fewer species. The former is seen as the result of the differential ability of lowland species to invade uplands, and the latter as a decrease in the kind and duration of frog-spawning sites. Reduced equitability with increasing elevation is principally due to the much greater proportional increase of the commonest species. In the evolution of American and Bornean-Philippine wet lowland faunas, frogs with direct development (Eleutherodactylus) have radiated in the former in the same fashion that skinks have in the latter.

Biotropica↗

USGS2020

Daily nest predation rates decrease with body size in passerine birds

Body size evolution is generally framed by the benefits of being large, while costs are largely overlooked. An important putative cost of being large is the need to extend development periods, which should increase exposure to predation and potentially select against larger size. In birds, this selection pressure can be important because predation is the main source of offspring mortality and predators should more readily detect the larger nests associated with larger body sizes. Here, we show for diverse passerine birds across the world that counter to expectations, larger species suffer lower daily nest predation rates than smaller species. This pattern is consistent despite latitudinal variation in predation and does not seem to reflect a tendency of larger species to use more protected nests or less exposed nest locations. Evidence instead suggests that larger species attack a wider array of predator sizes, which could reduce predation rates in nests of large-bodied species. Regardless of the mechanism, the lower daily nest predation rates of larger species yield slightly lower predation rates over the entire development period compared with smaller species. These results highlight the importance of behavior as a mechanism to alter selection pressures and have implications for body size evolution.

The American Naturalist↗