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USGS2015

Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction

The reintroduction of a species into its historic range is a critical component of conservation programmes designed to restore extirpated metapopulations. However, many reintroduction efforts fail, and the lack of rigorous monitoring programmes and statistical models have prevented a general understanding of the factors affecting metapopulation viability following reintroduction. Spatially explicit metapopulation theory provides the basis for understanding the dynamics of fragmented populations linked by dispersal, but the theory has rarely been used to guide reintroduction programmes because most spatial metapopulation models require presence–absence data from every site in the network, and they do not allow for observation error such as imperfect detection. We develop a spatial occupancy model that relaxes these restrictive assumptions and allows for inference about metapopulation extinction risk and connectivity. We demonstrate the utility of the model using six years of data on the Chiricahua leopard frog Lithobates chiricahuensis , a threatened desert-breeding amphibian that was reintroduced to a network of sites in Arizona USA in 2003. Our results indicate that the model can generate precise predictions of extinction risk and produce connectivity maps that can guide conservation efforts following reintroduction. In the case of L. chiricahuensis , many sites were functionally isolated, and 82% of sites were characterized by intermittent water availability and high local extinction probabilities (0·84, 95% CI: 0·64–0·99). However, under the current hydrological conditions and spatial arrangement of sites, the risk of metapopulation extinction is estimated to be <3% over a 50-year time horizon. Low metapopulation extinction risk appears to result from the high dispersal capability of the species, the high density of sites in the region and the existence of predator-free permanent wetlands with low local extinction probabilities. Should management be required, extinction risk can be reduced by either increasing the hydroperiod of existing sites or by creating new sites to increase connectivity. Synthesis and applications . This work demonstrates how spatio-temporal statistical models based on ecological theory can be applied to forecast the outcomes of conservation actions such as reintroduction. Our spatial occupancy model should be particularly useful when management agencies lack the funds to collect intensive individual-level data.

Arizona, New Mexico↗

USGS2022

Combining fixed-location count data and movement data to estimate abundance of a lake sturgeon spawning run

Estimating abundance of migrating fishes is challenging. While sonars can be deployed continuously, improper assumptions about unidirectional migration and complete spatial coverage can lead to inaccurate estimates. To address these challenges, we present a framework for combining fixed-location count data from a dual-frequency identification sonar (DIDSON) with movement data from acoustic telemetry to estimate spawning run abundance of lake sturgeon ( Acipenser fulvescens ). Acoustic telemetry data were used to estimate the probability of observing a lake sturgeon on the DIDSON and to determine the probability that a lake sturgeon passing the DIDSON site had passed the site previously during the season. Combining probabilities with DIDSON counts, using a Bayesian integrated model, we estimated the following abundances: 99 (42–215 credible interval, CI) in 2017, 131 (82–248 CI) in 2018, and 92 (47–184 CI) in 2019. Adding movement data generated better inferences on count data by incorporating fish behavior (e.g., multiple migrations in a single season) and its uncertainty into abundance estimates. This framework can be applied to count and movement data to estimate abundance of spawning runs of other migratory fishes in riverine systems.

Vermont↗

USGS2018

Full-range, solar-reflected hyperspectral microscopy to support earth remote sensing research

Over the past 20 years, hyperspectral microscopy has grown into a robust field of analysis for a number of applications. The visible to near-infrared (VNIR; 400 to 1000 nm) region of the spectrum has demonstrated utility for the characterization of healthy and diseased tissue and of biomolecular indicators at the cellular level. Here, we describe the development of a hyperspectral imaging (HSI) microscope that is aimed at material characterization to complement traditional stand-off, earth remote sensing with hyperspectral sensors. We combine commercial off the shelf technology to build an HSI microscope to collect spectral data with illumination provided by a tunable laser. Hyperspectral imaging microscopy (HIM) facilitates detailed examination of target materials at the subcentimeter spatial scale. The custom-built, laser illumination HSI microscope covers the NIR to shortwave infrared (NIR/SWIR; 900 to 2500 nm) solar-reflected spectral range. It is combined with a separate VNIR sensor (400 to 900 nm) that utilizes quartz–tungsten–halogen lamps for illumination. The combined sensors provide a means to collect <10,000 s of spectra in the full VNIR/SWIR spectral range from both pure substances and precisely engineered linear and nonlinear mixtures. The large abundance of spectra allows for a more detailed understanding of the variability and multivariate probability distributions of spectral signatures. This additional information aids in understanding the variability observed in ground truth spectra collected from portable spectrometers, and it greatly enhances sample description and metadata content. In addition, HIM data cubes can serve as proxies, as “microscenes,” for systems engineering applications such as trade studies for HSI acquired by air- and space-borne sensors.

Journal of Applied Remote Sensing↗

USGS2023

Eruption of stagnant lava from an inactive perched lava lake

Lava flow hazards are usually thought to end when the erupting vent becomes inactive, but this is not always the case. At Kīlauea in August 2014, a spiny ʻaʻā flow erupted from the levee of a crusted perched lava lake that had been inactive for a month, and the surface of the lava lake subsided as the flow advanced downslope over the following few days. Topography constructed from oblique aerial photographs using structure-from-motion (SfM) software shows that the volume of the flow (∼68,000 m 3 ) closely matches the volume of subsidence of the crusted lava lake (∼64,000 m 3 ). The similarity of these volumes, along with the textural characteristics of the lava, shows that the lava that fed the flow had been stored beneath the surface of the perched lava lake, and that the flow was not generated by reactivation of the vent. This extends the duration of the local lava flow hazard presented by perched lava lakes and similar flow field structures that store lava, such as rootless shields. The flow probably occurred because the density of the lava beneath the crusted surface of the perched lava lake increased through loss of gas bubbles until it was able to penetrate the less-dense levee, which was composed of relatively vesicular overflows. The flow is thus equivalent to the lava seeps described previously at Kīlauea and elsewhere. We present a simple physical model for the pressure change at the base of a densifying body of lava, which we apply to this case study, and which could be applied to similar scenarios elsewhere.

Hawaii↗

USGS1996

Observations and analysis of self-similar branching topology in glacier networks

Glaciers, like rivers, have a branching structure which can be characterized by topological trees or networks. Probability distributions of various topological quantities in the networks are shown to satisfy the criterion for self-similarity, a symmetry structure which might be used to simplify future models of glacier dynamics. Two analytical methods of describing river networks, Shreve's random topology model and deterministic self-similar trees, are applied to the six glaciers of south central Alaska studied in this analysis. Self-similar trees capture the topological behavior observed for all of the glaciers, and most of the networks are also reasonably approximated by Shreve's theory.

Journal of Geophysical Research B: Solid Earth↗

USGS2001

Impact of competitor species composition on predicting diameter growth and survival rates of Douglas-fir trees in southwestern Oregon

Mixed conifer and hardwood stands in southwestern Oregon were studied to explore the hypothesis that competition effects on individual-tree growth and survival will differ according to the species comprising the competition measure. Likewise, it was hypothesized that competition measures should extrapolate best if crown-based surrogates are given preference over diameter-based (basal area based) surrogates. Diameter growth and probability of survival were modeled for individual Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) trees growing in pure stands. Alternative models expressing one-sided and two-sided competition as a function of either basal area or crown structure were then applied to other plots in which Douglas-fir was mixed with other conifers and (or) hardwood species. Crown-based variables outperformed basal area based variables as surrogates for one-sided competition in both diameter growth and survival probability, regardless of species composition. In contrast, two-sided competition was best represented by total basal area of competing trees. Surrogates reflecting differences in crown morphology among species relate more closely to the mechanics of competition for light and, hence, facilitate extrapolation to species combinations for which no observations are available.

Canadian Journal of Forest Research↗

USGS1983

Effects of roads on small mammals

(1) The study was designed to determine the effects of roads on the diversity, spatial distribution, and density of small mammals. (2) Forty species of small mammal (5859 individuals) were snap-trapped in the study. Data resulted from 144 360 trap-nights of effort for an average of 4.06 captures per 100 trap-nights. (3) Small mammal community structure and density were both influenced by roads. Community structure in right-of-way (ROW) habitat was different from that in adjacent habitat. Five species did not prefer ROW habitat: the golden mouse, dusky-footed woodrat, brush mouse, pinon mouse, and California red-backed vole. However, there were more species present in ROW habitat than in adjacent habitat. Grassland species generally preferred ROW habitat and many less habitat-specific species were distributed in ROW and adjacent habitat. (4) Small mammal density (all species combined) was greater in interstate ROW habitat than in adjacent habitat. This was also true individually for the eastern harvest mouse, white-footed mouse, meadow vole, prairie vole, vagrant shrew. Townsend's vole, and California vole. Small mammal density was less in county road ROWs than in adjacent habitat, probably because of the small size of these areas. The data indicate that ROW habitat and its accompanying edge are attractive no: only to grassland species but also to many less habitat-specific species that make use of the ROW-edge-adjacent habitat complex. (5) Mortality on interstate highways was greatest for those species with highest densities in ROW habitat, and did not appear to be detrimental to populations of these species.

Journal of Applied Ecology↗

USGS2008

Probabilistic seismic hazard in the San Francisco Bay area based on a simplified viscoelastic cycle model of fault interactions

We construct a viscoelastic cycle model of plate boundary deformation that includes the effect of time-dependent interseismic strain accumulation, coseismic strain release, and viscoelastic relaxation of the substrate beneath the seismogenic crust. For a given fault system, time-averaged stress changes at any point (not on a fault) are constrained to zero; that is, kinematic consistency is enforced for the fault system. The dates of last rupture, mean recurrence times, and the slip distributions of the (assumed) repeating ruptures are key inputs into the viscoelastic cycle model. This simple formulation allows construction of stress evolution at all points in the plate boundary zone for purposes of probabilistic seismic hazard analysis (PSHA). Stress evolution is combined with a Coulomb failure stress threshold at representative points on the fault segments to estimate the times of their respective future ruptures. In our PSHA we consider uncertainties in a four-dimensional parameter space: the rupture peridocities, slip distributions, time of last earthquake (for prehistoric ruptures) and Coulomb failure stress thresholds. We apply this methodology to the San Francisco Bay region using a recently determined fault chronology of area faults. Assuming single-segment rupture scenarios, we find that fature rupture probabilities of area faults in the coming decades are the highest for the southern Hayward, Rodgers Creek, and northern Calaveras faults. This conclusion is qualitatively similar to that of Working Group on California Earthquake Probabilities, but the probabilities derived here are significantly higher. Given that fault rupture probabilities are highly model-dependent, no single model should be used to assess to time-dependent rupture probabilities. We suggest that several models, including the present one, be used in a comprehensive PSHA methodology, as was done by Working Group on California Earthquake Probabilities.

Journal of Geophysical Research B: Solid Earth↗

USGS2022

Density surface and excursion sets modeling as an approach to estimating population densities

Effective species management and conservation require knowledge of species distribution and status. We used point-transect distance sampling surveys of the endangered palila ( Loxioides bailleui ), a honeycreeper currently found only on the Island of Hawai'i, USA, to generate robust estimates of total abundance and simultaneously model the distribution, abundance, and spatial correlation of the species as a density surface model (DSM). Point-transect distance sampling is a widely applied method to estimate bird densities accounting for imperfect detection probability. For the DSM we used a generalized additive model framework and soap film smoothers to control the effects of boundary features. This modeling approach allowed us to account for imperfect detection and propagate detection probability uncertainty. We compared the uncertainty in palila abundance estimates using standard point-transect distance sampling to estimates from the DSM. The DSM, accounting for both distance-sampling-derived detection probability variance and the generalized additive model density estimate variance, did not improve population estimator precision; however, it provided insight into the species' distribution, density, and uncertainty. We also applied excursion sets analysis to objectively identify areas where the species occurs in high densities. The 2017 global population of <2,000 individuals was limited to an excursion area of 1,500 ha. Our findings can help management and regulatory agencies by simultaneously mapping a species' distribution and density, improving survey protocols, and providing information important to species conservation.

Hawaii↗

USGS2010

Investigations of potential bias in the estimation of lambda using Pradel's (1996) model for capture-recapture data

Pradel's (1996) temporal symmetry model permitting direct estimation and modelling of population growth rate, u i , provides a potentially useful tool for the study of population dynamics using marked animals. Because of its recent publication date, the approach has not seen much use, and there have been virtually no investigations directed at robustness of the resulting estimators. Here we consider several potential sources of bias, all motivated by specific uses of this estimation approach. We consider sampling situations in which the study area expands with time and present an analytic expression for the bias in u i We next consider trap response in capture probabilities and heterogeneous capture probabilities and compute large-sample and simulation-based approximations of resulting bias in u i . These approximations indicate that trap response is an especially important assumption violation that can produce substantial bias. Finally, we consider losses on capture and emphasize the importance of selecting the estimator for u i that is appropriate to the question being addressed. For studies based on only sighting and resighting data, Pradel's (1996) u i ' is the appropriate estimator.

Journal of Applied Statistics↗

USGS2010

Challenges of DNA-based mark-recapture studies of American black bears

We explored whether genetic sampling would be feasible to provide a region-wide population estimate for American black bears ( Ursus americanus ) in the southern Appalachians, USA. Specifically, we determined whether adequate capture probabilities ( p >0.20) and population estimates with a low coefficient of variation (CV <20%) could be achieved given typical agency budget and personnel constraints. We extracted DNA from hair collected from baited barbed-wire enclosures sampled over a 10-week period on 2 study areas: a high-density black bear population in a portion of Great Smoky Mountains National Park and a lower density population on National Forest lands in North Carolina, South Carolina, and Georgia. We identified individual bears by their unique genotypes obtained from 9 microsatellite loci. We sampled 129 and 60 different bears in the National Park and National Forest study areas, respectively, and applied closed mark–recapture models to estimate population abundance. Capture probabilities and precision of the population estimates were acceptable only for sampling scenarios for which we pooled weekly sampling periods. We detected capture heterogeneity biases, probably because of inadequate spatial coverage by the hair-trapping grid. The logistical challenges of establishing and checking a sufficiently high density of hair traps make DNA-based estimates of black bears impractical for the southern Appalachian region. Alternatives are to estimate population size for smaller areas, estimate population growth rates or survival using mark–recapture methods, or use independent marking and recapturing techniques to reduce capture heterogeneity.

Georgia, North Carolina, South Carolina, Tennessee↗

USGS2009

Hydraulic anisotropy characterization of pneumatic-fractured sediments using azimuthal self potential gradient

The pneumatic fracturing technique is used to enhance the permeability and porosity of tight unconsolidated soils (e.g. clays), thereby improving the effectiveness of remediation treatments. Azimuthal self potential gradient (ASPG) surveys were performed on a compacted, unconsolidated clay block in order to evaluate their potential to delineate contaminant migration pathways in a mechanically-induced fracture network. Azimuthal resistivity (ARS) measurements were also made for comparative purposes. Following similar procedures to those used in the field, compressed kaolinite sediments were pneumatically fractured and the resulting fracture geometry characterized from strike analysis of visible fractures combined with strike data from optical borehole televiewer (BHTV) imaging. We subsequently injected a simulated treatment (electrolyte/dye) into the fractures. Both ASPG and ARS data exhibit anisotropic geoelectric signatures resulting from the fracturing. Self potentials observed during injection of electrolyte are consistent with electrokinetic theory and previous laboratory results on a fracture block model. Visual (polar plot) analysis and linear regression of cross plots show ASPG lobes are correlated with azimuths of high fracture strike density, evidence that the ASPG anisotropy is a proxy measure of hydraulic anisotropy created by the pneumatic fracturing. However, ARS data are uncorrelated with fracture strike maxima and resistivity anisotropy is probably dominated by enhanced surface conduction along azimuths of weak 'starter paths' formed from pulverization of the clay and increases in interfacial surface area. We find the magnitude of electrokinetic SP scales with the applied N2 gas pressure gradient (??PN2) for any particular hydraulically-active fracture set and that the positive lobe of the ASPG anomaly indicates the flow direction within the fracture network. These findings demonstrate the use of ASPG in characterizing the effectiveness of (1) pneumatic fracturing and (2) defining likely flow directions of remedial treatments in unconsolidated sediments and rock. ?? 2008 Elsevier B.V. All rights reserved.

Journal of Contaminant Hydrology↗

USGS1994

Falcon versus grouse: flight adaptations of a predator and its prey

Several falcons were trained to fly along a 500 m course to a lure. The air speeds of the more consistent performers averaged about 1.5 times their calculated minimum power speeds, and occasionally reached 2.1 times the minimum power speed. Wing beat frequencies of all the falcons were above those estimated from earlier field observations, and the same was true of wild Sage Grouse Centrocercus urophasianus, a regular falconer's quarry in the study area. Measurements of grouse killed by falcons showed that their wings were short, with broad slotted tips, whereas the falcons' wings were longer in relation to their body mass, and tapered. The short wings of grouse result in fast flight, high power requirements, and reduced capacity for aerobic flight. Calculations indicated that the grouse should fly faster than the falcons, and had the large amount of flight muscle needed to do so, but that the falcons would be capable of prolonged aerobic flight, whereas the grouse probably would not. We surmise that Sage Grouse cannot fly continuously without incurring an oxygen debt, and are therefore not long-distance migrants, although this limitation is partly due to their large size, and would not apply to smaller galliform birds such as ptarmigan Lagopus spp. The wing action seen in video recordings of the falcons was not consistent with the maintenance of constant circulation. We call it 'chase mode' because it appears to be associated with a high level of muscular exertion, without special regard to fuel economy. It shows features in common with the 'bounding' flight of passerines.

Journal of Avian Biology↗

USGS2015

Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer-aquitard complexes

This study evaluates the role of the Peclet number as affected by molecular diffusion in transient anomalous transport, which is one of the major knowledge gaps in anomalous transport, by combining Monte Carlo simulations and stochastic model analysis. Two alluvial settings containing either short- or long-connected hydrofacies are generated and used as media for flow and transport modeling. Numerical experiments show that 1) the Peclet number affects both the duration of the power-law segment of tracer breakthrough curves (BTCs) and the transition rate from anomalous to Fickian transport by determining the solute residence time for a given low-permeability layer, 2) mechanical dispersion has a limited contribution to the anomalous characteristics of late-time transport as compared to molecular diffusion due to an almost negligible velocity in floodplain deposits, and 3) the initial source dimensions only enhance the power-law tail of the BTCs at short travel distances. A tempered stable stochastic (TSS) model is then applied to analyze the modeled transport. Applications show that the time-nonlocal parameters in the TSS model relate to the Peclet number, P e . In particular, the truncation parameter in the TSS model increases nonlinearly with a decrease in P e due to the decrease of the mean residence time, and the capacity coefficient increases with an increase in molecular diffusion which is probably due to the increase in the number of immobile particles. The above numerical experiments and stochastic analysis therefore reveal that the Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer–aquitard complexes.

Journal of Contaminant Hydrology↗

USGS2011

Metacommunity theory as a multispecies, multiscale framework for studying the influence of river network structure on riverine communities and ecosystems

Explaining the mechanisms underlying patterns of species diversity and composition in riverine networks is challenging. Historically, community ecologists have conceived of communities as largely isolated entities and have focused on local environmental factors and interspecific interactions as the major forces determining species composition. However, stream ecologists have long embraced a multiscale approach to studying riverine ecosystems and have studied both local factors and larger-scale regional factors, such as dispersal and disturbance. River networks exhibit a dendritic spatial structure that can constrain aquatic organisms when their dispersal is influenced by or confined to the river network. We contend that the principles of metacommunity theory would help stream ecologists to understand how the complex spatial structure of river networks mediates the relative influences of local and regional control on species composition. From a basic ecological perspective, the concept is attractive because new evidence suggests that the importance of regional processes (dispersal) depends on spatial structure of habitat and on connection to the regional species pool. The role of local factors relative to regional factors will vary with spatial position in a river network. From an applied perspective, the long-standing view in ecology that local community composition is an indicator of habitat quality may not be uniformly applicable across a river network, but the strength of such bioassessment approaches probably will depend on spatial position in the network. The principles of metacommunity theory are broadly applicable across taxa and systems but seem of particular consequence to stream ecology given the unique spatial structure of riverine systems. By explicitly embracing processes at multiple spatial scales, metacommunity theory provides a foundation on which to build a richer understanding of stream communities.

Journal of the North American Benthological Societ↗

USGS2011

Estimating detection and density of the Andean cat in the high Andes

The Andean cat ( Leopardus jacobita ) is one of the most endangered, yet least known, felids. Although the Andean cat is considered at risk of extinction, rigorous quantitative population studies are lacking. Because physical observations of the Andean cat are difficult to make in the wild, we used a camera-trapping array to photo-capture individuals. The survey was conducted in northwestern Argentina at an elevation of approximately 4,200 m during October-December 2006 and April-June 2007. In each year we deployed 22 pairs of camera traps, which were strategically placed. To estimate detection probability and density we applied models for spatial capture-recapture using a Bayesian framework. Estimated densities were 0.07 and 0.12 individual/km 2 for 2006 and 2007, respectively. Mean baseline detection probability was estimated at 0.07. By comparison, densities of the Pampas cat ( Leopardus colocolo ), another poorly known felid that shares its habitat with the Andean cat, were estimated at 0.74–0.79 individual/km 2 in the same study area for 2006 and 2007, and its detection probability was estimated at 0.02. Despite having greater detectability, the Andean cat is rarer in the study region than the Pampas cat. Properly accounting for the detection probability is important in making reliable estimates of density, a key parameter in conservation and management decisions for any species.

High Andes↗

USGS2003

Support of total maximum daily load programs using spatially referenced regression models

The spatially referenced regressions on watershed attributes modeling approach, as applied to predictions of total nitrogen flux in three North Carolina river basins, addresses several information needs identified by a National Research Council evaluation of the total maximum daily load program. The model provides reach-level predictions of the probability of exceeding water-quality criteria, and estimates of total nitrogen budgets. Model estimates of point- and diffuse-source contributions and nitrogen loss rates in streams and reservoirs compared moderately well with literature estimates. Maps of reach-level predictions of nutrient inputs and delivery provide an intuitive and spatially detailed summary of the origins and fate of nutrients within a basin.

Journal of Water Resources Planning and Management↗

USGS2013

Bayesian inversion of data from effusive volcanic eruptions using physics-based models: Application to Mount St. Helens 2004--2008

Physics-based models of volcanic eruptions can directly link magmatic processes with diverse, time-varying geophysical observations, and when used in an inverse procedure make it possible to bring all available information to bear on estimating properties of the volcanic system. We develop a technique for inverting geodetic, extrusive flux, and other types of data using a physics-based model of an effusive silicic volcanic eruption to estimate the geometry, pressure, depth, and volatile content of a magma chamber, and properties of the conduit linking the chamber to the surface. A Bayesian inverse formulation makes it possible to easily incorporate independent information into the inversion, such as petrologic estimates of melt water content, and yields probabilistic estimates for model parameters and other properties of the volcano. Probability distributions are sampled using a Markov-Chain Monte Carlo algorithm. We apply the technique using GPS and extrusion data from the 2004–2008 eruption of Mount St. Helens. In contrast to more traditional inversions such as those involving geodetic data alone in combination with kinematic forward models, this technique is able to provide constraint on properties of the magma, including its volatile content, and on the absolute volume and pressure of the magma chamber. Results suggest a large chamber of >40 km 3 with a centroid depth of 11–18 km and a dissolved water content at the top of the chamber of 2.6–4.9 wt%.

Washington↗