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USGS2010

Polybaric evolution of phonolite, trachyte, and rhyolite volcanoes in eastern Marie Byrd Land, Antarctica: Controls on peralkalinity and silica saturation

In the Marie Byrd Land volcanic province, peralkaline and metaluminous trachytes, phonolites, and rhyolites occur in 18 large shield volcanoes that are closely associated in time and space. They are arrayed radially across an 800 km wide structural dome, with the oldest at the crest and the youngest around the flanks. Several lines of evidence suggest that these rocks evolved via opensystem, polybaric fractionation. We have used mass balance modeling of major elements together with trace-element data and mineral chemistry to help explain the evolution of this diverse suite of felsic rocks, which appear to have been generated coevally in isolated magma chambers, and erupted close to each other in patterns related to tectonic uplift and extension within the West Antarctic rift system. Isotopic and trace-element data indicate that this occurred with only minimal crustal contamination. We focus on volcanoes of the Executive Committee Range and Mount Murphy, where we find good representation of basalts and felsic rocks within a small area. Our results suggest that the felsic rocks were derived from basaltic magmas that differentiated at multiple levels during their passage to the surface: first to ferrogabbroic compositions near the base of the lithosphere, then to intermediate compositions near the base of the crust, and finally to felsic compositions in mid- to upper crustal reservoirs. The high-pressure history has been largely masked by low-pressure processes. The best indications of a high-pressure history are the mineral phases in cumulate nodules and their correlation with modeling results, with REE anomalies, and with the composition of an unusual gabbroic intrusion. Silica saturation characteristics are believed to have originated in magma chambers near the base of the crust, via fractionation of variable proportions of kaersutite and plagioclase. Development of peralkalinity in felsic rocks took place in upper crustal reservoirs by fractionating a high ratio of plagioclase to clinopyroxene under conditions of low pH 2 O. With increasing pH 2 O, the ratio plagioclase/clinopyroxene in the fractionated assemblage decreases and metaluminous liquids resulted. Crustal contamination seems to have had a role in suppressing peralkalinity , and was probably a factor in the origin of high- silica metaluminous rhyolite , but metaluminous rocks are uncommon. The volume and diversity of felsic rocks were probably enhanced by the structure of the lithosphere, the persistence of plume activity, and the immobility of the Antarctic plate. Mechanical boundaries at the base of the lithosphere and crust, and within the crust, appear to have acted as filters, trapping magmas at multiple levels, and prolonging the fractionation process. Final volumes would have been further enhanced by repeated refluxing of the same magma chambers, controlled by plume activity and plate immobility.

International Geology Review↗
USGS2014

40Ar/39Ar Geochronology, Isotope Geochemistry (Sr, Nd, Pb), and petrology of alkaline lavas near Yampa, Colorado: migration of alkaline volcanism and evolution of the northern Rio Grande rift

Volcanic rocks near Yampa, Colorado (USA), represent one of several small late Miocene to Quaternary alkaline volcanic fields along the northeast margin of the Colorado Plateau. Basanite, trachybasalt, and basalt collected from six sites within the Yampa volcanic field were investigated to assess correlations with late Cenozoic extension and Rio Grande rifting. In this paper we report major and trace element rock and mineral compositions and Ar, Sr, Nd, and Pb isotope data for these volcanic rocks. High-precision 40Ar/39Ar geochronology indicates westward migration of volcanism within the Yampa volcanic field between 6 and 4.5 Ma, and the Sr, Nd, and Pb isotope values are consistent with a primary source in the Proterozoic subcontinental lithospheric mantle. Relict olivine phenocrysts have Mg- and Ni-rich cores, whereas unmelted clinopyroxene cores are Na and Si enriched with finely banded Ca-, Mg-, Al-, and Ti-enriched rims, thus tracing their crystallization history from a lithospheric mantle source region to one in contact with melt prior to eruption. A regional synthesis of Neogene and younger volcanism within the Rio Grande rift corridor, from northern New Mexico to southern Wyoming, supports a systematic overall southwest migration of alkaline volcanism. We interpret this Neogene to Quaternary migration of volcanism toward the northeast margin of the Colorado Plateau to record passage of melt through subvertical zones within the lithosphere weakened by late Cenozoic extension. If the locus of Quaternary alkaline magmatism defines the current location of the Rio Grande rift, it includes the Leucite Hills, Wyoming. We suggest that alkaline volcanism in the incipient northern Rio Grande rift, north of Leadville, Colorado, represents melting of the subcontinental lithospheric mantle in response to transient infiltration of asthenospheric mantle into deep, subvertical zones of dilational crustal weakness developed during late Cenozoic extension that have been migrating toward, and subparallel to, the northeast margin of the Colorado Plateau since the middle Miocene. Quaternary volcanism within this northern Rio Grande rift corridor is evidence that the rift is continuing to evolve.

Colorado↗
USGS2010

Cenozoic plate motions and the volcano-tectonic evolution of western Oregon and Washington

A refined northeast Pacific plate-motion model provides a framework for analysis of the Tertiary volcanic and tectonic history of western Oregon and Washington. We examine three possible models for the origin of the allochthonous Paleocene and Eocene oceanic basalt basement of the Coast Range: (1) accretion to the continent of hot spot generated linear seamount chains; (2) accretion of thick oceanic crust and seamounts generated during Farallon-Kula spreading reorganizations between 61 and 48 Ma; and (3) eruption of basalt during oblique rifting of the continental margin as it overrode an active Yellowstone hot spot on the Kula-Farallon ridge. The plate model suggests that microplate rotation and accretion of hot spot generated linear aseismic ridges cannot be easily reconciled with rapid northeast motion of the KuIa and Farallon plates and the well-established paleomagnetic rotations. Following emplacement of the Coast Range basement, changes in the character of forearc, back arc and Cascade arc volcanism correlate with a marked decrease in the rate of Farallon-North America convergence between 43 and and 28 Ma. This slowdown may be responsible for (1) westward stepping of the volcanic arc front from the Challis axis to a Cascade axis at about 42 Ma; (2) a subsequent episode of increased ash flow tuff volcanism and extension in the Cascade arc between 37 and 18 Ma that correlates with the “ignimbrite flare-up” in the Basin and Range; and (3) a period of extensional basaltic and alkalic volcanism and intrusion in the Coast Range between 44 and 28 Ma. Reduction of the convergence rate and westward stepping of the flexure in the subducted slab may have reduced the horizontal compressive stress on the continent, allowing increased injection of magma into the crust, development of large, shallow magma chambers, and the outbreak of extensional volcanism over a large area behind the Farallon-North America subduction zone.

Oregon, Washington↗
USGS2022

Gaussian process forecasts Pseudogymnoascus destructans will cover coterminous United States by 2030

White-nose syndrome has been decimating populations of several bat species since its first occurrence in the Northeastern United States in the winter 2006–2007. The spread of the disease has been monitored across the continent through the collaboration of many organizations. Inferring the rate of spread of the disease and predicting its arrival at new locations is critical when assessing the current and predicting the future status and trends of bat species. We developed a model of disease spread that simultaneously achieves high-predictive performance, computational efficiency, and interpretability. We modeled white-nose syndrome spread using Gaussian process variations to infer the spread rate of the disease front, identify areas of anomalous time of arrival, and provide future forecasts of the expected time of arrival throughout North America. Cross-validation of model predictive performance identified a stationary Gaussian process without an additional residual error process as the best-supported model. Results indicated that white-nose syndrome is likely to spread throughout the entire continental United States by 2030. These annually updatable model predictions will be useful in determining the horizon over which disease management actions must take place as well as in status and trend assessments of disease-affected bats.

Ecology and Evolution↗
USGS2017

Long-term video surveillance and automated analyses reveal arousal patterns in groups of hibernating bats

Understanding natural behaviours is essential to determining how animals deal with new threats (e.g. emerging diseases). However, natural behaviours of animals with cryptic lifestyles, like hibernating bats, are often poorly characterized. White-nose syndrome (WNS) is an unprecedented disease threatening multiple species of hibernating bats, and pathogen-induced changes to host behaviour may contribute to mortality. To better understand the behaviours of hibernating bats and how they might relate to WNS, we developed new ways of studying hibernation across entire seasons. We used thermal-imaging video surveillance cameras to observe little brown bats ( Myotis lucifugus ) and Indiana bats ( M. sodalis ) in two caves over multiple winters. We developed new, sharable software to test for autocorrelation and periodicity of arousal signals in recorded video. We processed 740 days (17,760 hr) of video at a rate of >1,000 hr of video imagery in less than 1 hr using a desktop computer with sufficient resolution to detect increases in arousals during midwinter in both species and clear signals of daily arousal periodicity in infected M. sodalis . Our unexpected finding of periodic synchronous group arousals in hibernating bats demonstrate the potential for video methods and suggest some bats may have innate behavioural strategies for coping with WNS. Surveillance video and accessible analysis software make it now practical to investigate long-term behaviours of hibernating bats and other hard-to-study animals.

Methods in Ecology and Evolution↗
USGS2013

Compaction and gas loss in welded pyroclastic deposits as revealed by porosity, permeability, and electrical conductivity measurements of the Shevlin Park Tuff

Pyroclastic flows produced by large volcanic eruptions commonly densify after emplacement. Processes of gas escape, compaction, and welding in pyroclastic-flow deposits are controlled by the physical and thermal properties of constituent material. Through measurements of matrix porosity, permeability, and electrical conductivity, we provide a framework for understanding the evolution of pore structure during these processes. Using data from the Shevlin Park Tuff in central Oregon, United States, and from the literature, we find that over a porosity range of 0%–70%, matrix permeability varies by almost 10 orders of magnitude (from 10 –20 to 10 –11 m 2 ), with over three orders of magnitude variation at any given porosity. Part of the variation at a given porosity is due to permeability anisotropy, where oriented core samples indicate higher permeabilities parallel to foliation (horizontally) than perpendicular to foliation (vertically). This suggests that pore space is flattened during compaction, creating anisotropic crack-like networks, a geometry that is supported by electrical conductivity measurements. We find that the power law equation: k 1 = 1.3 × 10 –21 × ϕ 5.2 provides the best approximation of dominant horizontal gas loss, where k 1 = permeability, and ϕ = porosity. Application of Kozeny-Carman fluid-flow approximations suggests that permeability in the Shevlin Park Tuff is controlled by crack- or disk-like pore apertures with minimum widths of 0.3 and 7.5 μm. We find that matrix permeability limits compaction over short times, but deformation is then controlled by competition among cooling, compaction, water resorption, and permeable gas escape. These competing processes control the potential for development of overpressure (and secondary explosions) and the degree of welding in the deposit, processes that are applicable to viscous densification of volcanic deposits in general. Further, the general relationships among porosity, permeability, and pore geometry are relevant for flow of any fluid through an ignimbritic host.

Oregon↗
USGS2015

Uranium isotopes and dissolved organic carbon in loess permafrost: Modeling the age of ancient ice

The residence time of ice in permafrost is an indicator of past climate history, and of the resilience and vulnerability of high-latitude ecosystems to global change. Development of geochemical indicators of ground-ice residence times in permafrost will advance understanding of the circumstances and evidence of permafrost formation, preservation, and thaw in response to climate warming and other disturbance. We used uranium isotopes to evaluate the residence time of segregated ground ice from ice-rich loess permafrost cores in central Alaska. Activity ratios of 234 U vs. 238 U ( 234 U/ 238 U) in water from thawed core sections ranged between 1.163 and 1.904 due to contact of ice and associated liquid water with mineral surfaces over time. Measured ( 234 U/ 238 U) values in ground ice showed an overall increase with depth in a series of five neighboring cores up to 21 m deep. This is consistent with increasing residence time of ice with depth as a result of accumulation of loess over time, as well as characteristic ice morphologies, high segregated ice content, and wedge ice, all of which support an interpretation of syngenetic permafrost formation associated with loess deposition. At the same time, stratigraphic evidence indicates some past sediment redistribution and possibly shallow thaw among cores, with local mixing of aged thaw waters. Using measures of surface area and a leaching experiment to determine U distribution, a geometric model of ( 234 U/ 238 U) evolution suggests mean ages of up to ∼200 ky BP in the deepest core, with estimated uncertainties of up to an order of magnitude. Evidence of secondary coatings on loess grains with elevated ( 234 U/ 238 U) values and U concentrations suggests that refinement of the geometric model to account for weathering processes is needed to reduce uncertainty. We suggest that in this area of deep ice-rich loess permafrost, ice bodies have been preserved from the last glacial period (10–100 ky BP), despite subsequent fluctuations in climate, fire disturbance and vegetation. Radiocarbon ( 14 C) analysis of dissolved organic carbon (DOC) in thaw waters supports ages greater than ∼40 ky BP below 10 m. DOC concentrations in thaw waters increased with depth to maxima of >1000 ppm, despite little change in ice content or cryostructures. These relations suggest time-dependent production of old DOC that will be released upon permafrost thaw at a rate that is mediated by sediment transport, among other factors.

Alaska↗
USGS2003

Integrating soils and geomorphology in mountains - An example from the Front Range of Colorado

Soil distribution in high mountains reflects the impact of several soil-forming factors. Soil geomorphologists use key pedological properties to estimate ages of Quaternary deposits of various depositional environments, estimate long-term stability and instability of landscapes, and make inferences on past climatic change. Once the influence of the soil-forming factors is known, soils can be used to help interpret some aspects of landscape evolution that otherwise might go undetected. The Front Range of Colorado rises from the plains of the Colorado Piedmont at about 1700 m past a widespread, dissected Tertiary erosion surface between 2300 and 2800 m up to an alpine Continental Divide at 3600 to over 4000 m. Pleistocene valley glaciers reached the western edge of the erosion surface. Parent rocks are broadly uniform (granitic and gneissic). Climate varies from 46 cm mean annual precipitation (MAP) and 11 ??C mean annual temperature (MAT) in the plains to 102 cm and -4 ??C, respectively, near the range crest. Vegetation follows climate with grassland in the plains, forest in the mountains, and tundra above 3450 m. Soils reflect the bioclimatic transect from plains to divide: A/Bw or Bt/Bk or K (grassland) to A/E/Bw or Bt/C (forest) to A/Bw/C (tundra). Corresponding soil pH values decrease from 8 to less than 5 with increasing elevation. The pedogenic clay minerals dominant in each major vegetation zone are: smectite (grassland), vermiculite (forest), and 1.0-1.8 nm mixed-layer clays (tundra). Within the lower forested zone, the topographic factor (aspect) results in more leached, colder soils, with relatively thin O horizons, well-expressed E horizons and Bt horizons (Alfisols) on N-facing slopes, whereas soils with thicker A horizons, less developed or no E horizons, and Bw or Bt horizons (Mollisols) are more common on S-facing slopes. The topographic factor in the tundra results in soil patterns as a consequence of wind-redistributed snow and the amount of time it lingers on the landscape. An important parent material factor is airborne dust, which results in fine-grained surface horizons and, if infiltrated, contributes to clay accumulation in some Bt horizons. The time factor is evaluated by soil chronosequence studies of Quaternary deposits in tundra, upper forest, and plains grassland. Few soils in the study area are >10,000 years old in the tundra, >100,000 years old in the forest, and >2 million years old in the grassland. Stages of granite weathering vary with distance from the Continental Divide and the best developed is grus near the sedimentary/granitic rock contact just west of the mountain front. Grus takes a minimum of 100,000 years to form. Some of the relations indicated by the soil map patterns are: (1) parts of the erosion surface have been stable for 100,000 years or more; (2) development of grus near the mountain front could be due in part to pre-Pennsylvanian weathering; (3) a few soil properties reflect Quaternary paleoclimate; and (4) a correlation between soil development in the canyons and stream incision rates. ?? 2003 Elsevier Science B.V. All rights reserved.

Geomorphology↗
USGS2017

Developing approaches for linear mixed modeling in landscape genetics through landscape-directed dispersal simulations

Dispersal can impact population dynamics and geographic variation, and thus, genetic approaches that can establish which landscape factors influence population connectivity have ecological and evolutionary importance. Mixed models that account for the error structure of pairwise datasets are increasingly used to compare models relating genetic differentiation to pairwise measures of landscape resistance. A model selection framework based on information criteria metrics or explained variance may help disentangle the ecological and landscape factors influencing genetic structure, yet there are currently no consensus for the best protocols. Here, we develop landscape-directed simulations and test a series of replicates that emulate independent empirical datasets of two species with different life history characteristics (greater sage-grouse; eastern foxsnake). We determined that in our simulated scenarios, AIC and BIC were the best model selection indices and that marginal R 2 values were biased toward more complex models. The model coefficients for landscape variables generally reflected the underlying dispersal model with confidence intervals that did not overlap with zero across the entire model set. When we controlled for geographic distance, variables not in the underlying dispersal models (i.e., nontrue) typically overlapped zero. Our study helps establish methods for using linear mixed models to identify the features underlying patterns of dispersal across a variety of landscapes.

Ecology and Evolution↗
USGS2003

Gold deposits in metamorphic belts: Overview of current understanding, outstanding problems, future research, and exploration significance

Metamorphic belts are complex regions where accretion or collision has added to, or thickened, continental crust. Gold-rich deposits can be formed at all stages of orogen evolution, so that evolving metamorphic belts contain diverse gold deposit types that may be juxtaposed or overprint each other. This partly explains the high level of controversy on the origin of some deposit types, particularly those formed or overprinted/remobilized during the major compressional orogeny that shaped the final geometry of the hosting metamorphic belts. These include gold-dominated orogenic and intrusion-related deposits, but also particularly controversial gold deposits with atypical metal associations. There are a number of outstanding problems for all types of gold deposits in metamorphc belts. These include the following: (1) definitive classifications, (2) unequivocal recognition of fluid and metal sources, (3) understanding of fluid migration and focusing at all scales, (4) resolution of the precise role of granitoid magmatism, (5) precise gold-depositional mechanisms, particularly those producing high gold grades, and (6) understanding of the release of CO2-rich fluids from subducting slabs and subcreted oceanic crust and granitoid magmas at different crustal levels. Research needs to be better coordinated and more integrated, such that detailed fluid-inclusion, trace-element, and isotopic studies of both gold deposits and potential source rocks, using cutting-edge technology, are embedded in a firm geological framework at terrane to deposit scales. Ultimately, four-dimensional models need to be developed, involving high-quality, three-dimensional geological data combined with integrated chemical and fluid-flow modeling, to understand the total history of the hydrothermal systems involved. Such research, particularly that which can predict superior targets visible in data sets available to exploration companies before discovery, has obvious spin-offs for global- to deposit-scale targeting of deposits with superior size and grade in the covered terranes that will be the exploration focus of the twenty-first century.

Economic Geology↗
USGS1987

Movement and fate of crude-oil in contaminants in the subsurface environment at Bemidji, Minnesota: Chapter C in U.S. Geological Survey program on toxic waste--ground-water contamination: Proceedings of the Third technical meeting, Pensacola, Florida, March 23-27, 1987

On August 20, 1979, a pipeline break in a remote area near Bemidji, Minn. (fig. C-l), resulted in the release of 1.5x10 5 L (liters) of crude oil. Although about 1.1x10 5 L were removed from the site as part of the cleanup, some crude oil infiltrated the ground and percolated to the water table. The spill occurred in the recharge area of a local flow system that discharges to a small lake 300 m (meters) downgradient (Hult, 1984). The aquifer is a pitted and dissected outwash plain underlain at a depth of about 20 m by low-permeability till. Crude oil is floating on the water table about 8 m below land surface and has migrated about 20 m as a separate fluid phase. Soluble petroleum derivatives have dissolved in and are moving with ground water. Volatile constituents are migrating through the unsaturated zone by diffusion. The abstracts presented in this chapter provide an overview of ongoing efforts to combine the results of interdependent, interdisciplinary research into the comprehensive understanding of the physical, chemical, and biological processes that will be needed to develop predictive models of contaminant mobilization, transport, and fate. Franzi investigates the relationship between depositional and post-depositional processes and the heterogeneity and anisotropy of the aquifer. Post-depositional subsidence and collapse caused by melting of stagnant ice has created significant geomorphic and hydrogeologic structures. Miller describes a preliminary ground-water flow and chemical-transport model used to assess the effect of these hydrologic discontinuities, estimate aquifer properties, and to guide continuing field work. Abstracts by Siegel, Bennett, and Berndt describe studies of dissolved inorganic constituents and parameters done to characterize the geochemical environments in and around the site. An anoxic zone, probably plume shaped, extends downgradient of the oil pool and into an oxic zone that surrounds the contamination. Carbonate minerals are actively dissolving in the oxic spray zone upgradient of the oil pool where oil is being mineralized, whereas quartz is dissolving underneath the oil by organic-acid complexation. Selective leaching experiments show that fractionation of metals is also occurring where the aquifer matrix is contaminated. Morphological analysis of quartz sand grains clearly show unusual rock-water interactions are occurring in the anaerobic contaminant zone. Preliminary analysis indicates the possibility of an organic/quartz interaction that is significantly increasing the mobility of silica through the system. Predictions of the evolution and ultimate geometry of contaminant plumes resulting from spills require quantitative descriptions of the rate of mass transfer from the organic fluid to ground water. Pfannkuch presents laboratory and field work that describe how the the rate of oil dissolution, and therefore the strength of the contaminant source, is controlled by fluctuations in ground-water velocity and water-table fluctuations.

Minnesota↗
USGS2021

Integrating environmental DNA results with diverse data sets to improve biosurveillance of river health

Autonomous, robotic environmental (e)DNA samplers now make it possible for biological observations to match the scale and quality of abiotic measurements collected by automated sensor networks. Merging these automated data streams may allow for improved insight into biotic responses to environmental change and stressors. Here, we merged eDNA data collected by robotic samplers installed at three U.S. Geological Survey (USGS) streamgages with gridded daily weather data, and daily water quality and quantity data into a cloud-hosted database. The eDNA targets were a rare fish parasite and a more common salmonid fish. We then used computationally expedient Bayesian hierarchical occupancy models to evaluate associations between abiotic conditions and eDNA detections and to simulate how uncertainty in result interpretation changes with the frequency of autonomous robotic eDNA sample collection. We developed scripts to automate data merging, cleaning and analysis steps into a chained-step, workflow. We found that inclusion of abiotic covariates only provided improved insight for the more common salmonid fish since its DNA was more frequently detected. Rare fish parasite DNA was infrequently detected, which caused occupancy parameter estimates and covariate associations to have high uncertainty. Our simulations found that collecting samples at least once per day resulted in more detections and less parameter uncertainty than less frequent sampling. Our occupancy and simulation results together demonstrate the advantages of robotic eDNA samplers and how these samples can be combined with easy to acquire, publicly available data to foster real-time biosurveillance and forecasting.

Idaho, Wyoming, Montana↗
USGS2011

PQLX: A seismic data quality control system description, applications, and users manual

We present a detailed description and users manual for a new tool to evaluate seismic station performance and characteristics by providing quick and easy transitions between visualizations of the frequency and time domains. The software is based on the probability density functions (PDF) of power spectral densities (PSD) (McNamara and Buland, 2004) and builds on the original development of the PDF stand-alone software system (McNamara and Boaz, 2005) and the seismological data viewer application PQL (IRIS-PASSCAL Quick Look) and PQLII (available through the IRIS PASSCAL program: http://www.passcal.nmt.edu/content/pql-ii-program-viewing-data). With PQLX (PQL eXtended), computed PSDs are stored in a MySQL database, allowing a user to access specific time periods of PSDs (PDF subsets) and time series segments through a GUI-driven interface. The power of the method and software lies in the fact that there is no need to screen the data for system transients, earthquakes, or general data artifacts, because they map into a background probability level. In fact, examination of artifacts related to station operation and episodic cultural noise allow us to estimate both the overall station quality and a baseline level of Earth noise at each site. The output of this analysis tool is useful for both operational and scientific applications. Operationally, it is useful for characterizing the current and past performance of existing broadband stations, for conducting tests on potential new seismic station locations, for evaluating station baseline noise levels (McNamara and others, 2009), for detecting problems with the recording system or sensors, and for evaluating the overall quality of data and metadata. Scientifically, the tool allows for mining of PSDs for investigations on the evolution of seismic noise (for example, Aster and others, 2008; and Aster and others, 2010) and other phenomena. Currently, PQLX is operational at several organizations including the USGS National Earthquake Information Center (NEIC), the USGS Albuquerque Seismological Laboratory (ASL), and the Incorporated Research Institutions in Seismology (IRIS) Data Management Center (DMC) for station monitoring and instrument response quality control. The PQLX system is available to the community at large through the U.S. Geological Survey (USGS) (http://ehpm-earthquake.wr.usgs.gov/research/software/pqlx.php) and IRIS (http://www.iris.edu/software/pqlx). Also provided is a fully searchable website for bug reporting and enhancement requests (http://wush.net/bugzilla/PQLX). The first part of this document aims to describe and illustrate some of the features and capabilities of the software. The second part of this document is a detailed users manual that covers installation procedures, system requirements, operations, bug reporting, and software components (Appendix).

Open-File Report↗
USGS2014

Reproductive ecology of lampreys

Lampreys typically spawn in riffle habitats during the spring. Spawning activity and diel (i.e., during daylight and at night) behavioral patterns are initiated when spring water temperatures increase to levels that coincide with optimal embryologic development. Nests are constructed in gravel substrate using the oral disc to move stones and the tail to fan sediment out of the nest. Spawning habitat used by individual species is generally a function of adult size, where small-bodied species construct nests in shallower water with slower flow and smaller gravel than large-bodied species. The mating system of lampreys is primarily polygynandrous (i.e., where multiple males mate with multiple females). Lamprey species with adult total length less than 30 cm generally spawn communally, where a nest may contain 20 or more individuals of both sexes. Lamprey species with adult sizes greater than 35 cm generally spawn in groups of two to four. Operational sex ratios of lampreys are highly variable across species, populations, and time, but are generally male biased. The act of spawning typically starts with the male attaching with his oral disc to the back of the female’s head; the male and female then entwine and simultaneously release gametes. However, alternative mating behaviors (e.g., release of gametes without paired courtship and sneaker males) have been observed. Future research should determine how multiple modalities of communication among lampreys (including mating pheromones) are integrated to inform species recognition and mate choice. Such research could inform both sea lamprey control strategies and provide insight into possible evolution of reproductive isolation mechanisms between paired lamprey species in sympatry.

Book chapter↗
USGS2011

Spatial capture-recapture models for search-encounter data

1. Spatial capture–recapture models make use of auxiliary data on capture location to provide density estimates for animal populations. Previously, models have been developed primarily for fixed trap arrays which define the observable locations of individuals by a set of discrete points. 2. Here, we develop a class of models for 'search-encounter' data, i.e. for detections of recognizable individuals in continuous space, not restricted to trap locations. In our hierarchical model, detection probability is related to the average distance between individual location and the survey path. The locations are allowed to change over time owing to movements of individuals, and individual locations are related formally by a model describing individual activity or home range centre which is itself regarded as a latent variable in the model. We provide a Bayesian analysis of the model in WinBUGS, and develop a custom MCMC algorithm in the R language. 3. The model is applied to simulated data and to territory mapping data for the Willow Tit from the Swiss Breeding Bird Survey MHB. While the observed density was 15 territories per nominal 1 km 2 plot of unknown effective sample area, the model produced a density estimate of 21∙12 territories per square km (95% posterior interval: 17–26). 4. Spatial capture–recapture models are relevant to virtually all animal population studies that seek to estimate population size or density, yet existing models have been proposed mainly for conventional sampling using arrays of traps. Our model for search-encounter data, where the spatial pattern of searching can be arbitrary and may change over occasions, greatly expands the scope and utility of spatial capture–recapture models.

Methods in Ecology and Evolution↗
USGS2024

Uranium redox and deposition transitions embedded in deep-time geochemical models and mineral chemistry networks

Uranium (U) is an important global energy resource and a redox sensitive trace element that reflects changing environmental conditions and geochemical cycling. The redox evolution of U mineral chemistry can be interrogated to understand the formation and distribution of U deposits and the redox processes involved in U geochemistry throughout Earth history. In this study, geochemical modeling using thermodynamic data, and mineral chemistry network analysis are used to investigate U geochemistry and deposition through time. The number of U 6+ mineral localities surpasses the number of U 4+ mineral localities in the Paleoproterozoic. Moreover, the number of sedimentary U 6+ mineral localities increases earlier in the Phanerozoic than the number of U 4+ sedimentary mineral localities, likely due to the necessity of sufficient sedimentary organic matter to reduce U 6+ –U 4+ . Indeed, modeling calculations indicate that increased oxidative weathering due to surface oxygenation limited U 4+ uraninite (UO 2 ) formation from weathered granite and basalt. Louvain network community detection shows that U 6+ forms minerals with many more shared elements and redox states than U 4+ . The range of weighted Mineral Element Electronegativity Coefficient of Variation (wMEE CV ) values of U 6+ minerals increases through time, particularly during the Phanerozoic. Conversely, the range of wMEE CV values of U 4+ minerals is consistent through time due to the relative abundance of uraninite, coffinite, and brannerite. The late oxidation and formation of U 6+ minerals compared to S 6+ minerals illustrates the importance of the development of land plants, organic matter deposition, and redox-controlled U deposition from ground water in continental sediments during this time-period.

Geochemistry, Geophysics, Geosystems↗
USGS2022

Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: Prominence of thymus expression, immune and metabolic function, and regions of ancient synteny

Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat ( Lasiurus cinereus ) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch ( P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov–Smirnov test ( P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1 -like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.

PeerJ↗
USGS2017

Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?

The relationships among and within the families that comprise the orthopteran superfamily Stenopelmatoidea (suborder Ensifera) remain poorly understood. We developed a phylogenetic hypothesis based on Bayesian analysis of two nuclear ribosomal and one mitochondrial gene for 118 individuals (84 de novo and 34 from GenBank). These included Gryllacrididae from North, Central, and South America, South Africa and Madagascar, Australia and Papua New Guinea; Stenopelmatidae from North and Central America and South Africa; Anostostomatidae from North and Central America, Papua New Guinea, New Zealand, Australia, and South Africa; members of the Australian endemic Cooloola (three species); and a representative of Lezina from the Middle East. We also included representatives of all other major ensiferan families: Prophalangopsidae, Rhaphidophoridae, Schizodactylidae, Tettigoniidae, Gryllidae, Gryllotalpidae and Myrmecophilidae and representatives of the suborder Caelifera as outgroups. Bayesian analyses of concatenated sequence data supported a clade of Stenopelmatoidea inclusive of all analyzed members of Gryllacrididae, Stenopelmatidae, Anostostomatidae, Lezina and Cooloola. We found Gryllacrididae worldwide to be monophyletic, while we did not recover a monophyletic Stenopelmatidae nor Anostostomatidae. Australian Cooloola clustered in a clade composed of Australian, New Zealand, and some (but not all) North American Anostostomatidae. Lezina was included in a clade of New World Anostostomatidae. Finally, we compiled and compared karyotypes and sound production characteristics for each supported group. Chromosome number, centromere position, drumming, and stridulation differed among some groups, but also show variation within groups. This preliminary trait information may contribute toward future studies of trait evolution. Despite greater taxon sampling within Stenopelmatoidea than previous efforts, some relationships among the families examined continue to remain elusive.

Zootaxa↗