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Results for “Diversity and Distributions”

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At least 1,153 records · Page 64Linked to original sources

USGS2017

DNA-based detection of the fungal pathogen Geomyces destructans in soil from bat hibernacula

White-nose syndrome (WNS) is an emerging disease causing unprecedented morbidity and mortality among bats in eastern North America. The disease is characterized by cutaneous infection of hibernating bats by the psychrophilic fungus Geomyces destructans . Detection of G. destructans in environments occupied by bats will be critical for WNS surveillance, management and characterization of the fungal lifecycle. We initiated an rRNA gene region-based molecular survey to characterize the distribution of G. destructans in soil samples collected from bat hibernacula in the eastern United States with an existing PCR test. Although this test did not specifically detect G. destructans in soil samples based on a presence/absence metric, it did favor amplification of DNA from putative Geomyces species. Cloning and sequencing of PCR products amplified from 24 soil samples revealed 74 unique sequence variants representing 12 clades. Clones with exact sequence matches to G. destructans were identified in three of 19 soil samples from hibernacula in states where WNS is known to occur. Geomyces destructans was not identified in an additional five samples collected outside the region where WNS has been documented. This study highlights the diversity of putative Geomyces spp. in soil from bat hibernacula and indicates that further research is needed to better define the taxonomy of this genus and to develop enhanced diagnostic tests for rapid and specific detection of G. destructans in environmental samples.

Connecticut, Indiana, Kentucky, Massachusetts, Min↗

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↗

USGS2012

Predictions and retrodictions of the hierarchical representation of habitat in heterogeneous environments

Interaction between habitat and species is central in ecology. Habitat structure may be conceived as being hierarchical, where larger, more diverse, portions or categories contain smaller, more homogeneous portions. When this conceptualization is combined with the observation that species have different abilities to relate to portions of the habitat that differ in their characteristics, a number of known patterns can be derived and new patterns hypothesized. We propose a quantitative form of this habitat–species relationship by considering species abundance to be a function of habitat specialization, habitat fragmentation, amount of habitat, and adult body mass. The model reproduces and explains patterns such as variation in rank–abundance curves, greater variation and extinction probabilities of habitat specialists, discontinuities in traits (abundance, ecological range, pattern of variation, body size) among species sharing a community or area, and triangular distribution of body sizes, among others. The model has affinities to Holling's textural discontinuity hypothesis and metacommunity theory but differs from both by offering a more general perspective. In support of the model, we illustrate its general potential to capture and explain several empirical observations that historically have been treated independently.

Ecological Modelling↗

USGS2008

Quantile regression applied to spectral distance decay

Remotely sensed imagery has long been recognized as a powerful support for characterizing and estimating biodiversity. Spectral distance among sites has proven to be a powerful approach for detecting species composition variability. Regression analysis of species similarity versus spectral distance allows us to quantitatively estimate the amount of turnover in species composition with respect to spectral and ecological variability. In classical regression analysis, the residual sum of squares is minimized for the mean of the dependent variable distribution. However, many ecological data sets are characterized by a high number of zeroes that add noise to the regression model. Quantile regressions can be used to evaluate trend in the upper quantiles rather than a mean trend across the whole distribution of the dependent variable. In this letter, we used ordinary least squares (OLS) and quantile regressions to estimate the decay of species similarity versus spectral distance. The achieved decay rates were statistically nonzero (p < 0.01), considering both OLS and quantile regressions. Nonetheless, the OLS regression estimate of the mean decay rate was only half the decay rate indicated by the upper quantiles. Moreover, the intercept value, representing the similarity reached when the spectral distance approaches zero, was very low compared with the intercepts of the upper quantiles, which detected high species similarity when habitats are more similar. In this letter, we demonstrated the power of using quantile regressions applied to spectral distance decay to reveal species diversity patterns otherwise lost or underestimated by OLS regression. ?? 2008 IEEE.

IEEE Geoscience and Remote Sensing Letters↗

USGS2020

Simultaneous Middle Pleistocene eruption of three widespread tholeiitic basalts in northern California (USA): Insights into crustal magma transport in an actively extending back arc

Mapping and chronology are central to understanding spatiotemporal volcanic trends in diverse tectonic settings. The Cascades back arc in northern California (USA) hosts abundant lava flows and normal faults, but tholeiitic basalts older than 200 ka are difficult to discriminate by classic mapping methods. Paleomagnetism and chemistry offer independent means of correlating basalts, including the Tennant, Dry Lake, and Hammond Crossing basalt fields. Paleomagnetic analysis of these chemically similar basalts yield notable overlap, with statistical analysis yielding 7 chances in 1,000,000 that their similar mean remanent directions are random. These basalts also have overlapping 40 Ar/ 39 Ar ages of 272.5 ± 30.6 ka (Tennant), 305.8 ± 23.9 ka (Dry Lake), and 300.4 ± 15.2 and 322.6 ± 17.4 ka (Hammond Crossing). Chemical and paleomagnetic analyses indicate that these spatially distributed basalts represent simultaneous (<100 yr uncertainty) eruptions, and thus we use 305.5 ± 9.8 ka (weighted mean) as the eruption age. Their vents align on a N25°W trend over a distance of 39 km. Tennant erupted the largest volume (3.55 ± 0.75 km 3 ) at the highest elevation; both factors decay to the south-southeast at Dry Lake (0.75 ± 0.15 km 3 ) and Hammond Crossing (0.15 ± 0.05 km 3 ). We propose vertical magma ascent beneath the Tennant vent area, where the most evolved, high-SiO 2 magma erupted, with lateral dike propagation in the brittle crust. Propagation was near orthogonal to east-west extension (0.3–0.6 mm/yr) along north-northwest–trending normal faults.

California↗

USGS2015

Literature review of giant gartersnake ( Thamnophis gigas ) biology and conservation

This report reviews the available literature on giant gartersnakes ( Thamnophis gigas ) to compile existing information on this species and identify knowledge gaps that, if addressed, would help to inform conservation efforts for giant gartersnakes. Giant gartersnakes comprise a species of semi-aquatic snake precinctive to wetlands in the Central Valley of California. The diversion of surface water and conversion of wetlands to agricultural and other land uses resulted in the loss of more than 90 percent of natural giant gartersnake habitats. Because of this habitat loss, giant gartersnakes are now listed by the United States and California Endangered Species Acts as Threatened. Most extant populations occur in the rice-growing regions of the Sacramento Valley, which comprises the northern portion of the giant gartersnake’s former range. The huge demand for water in California for agriculture, industry, recreation, and other human consumption, combined with periodic severe drought, places remaining giant gartersnake habitats at increased risk of degradation and loss. This literature review summarizes the available information on giant gartersnake distribution, habitat relations, behavior, demography, and other aspects of its biology relevant to conservation. This information is then compiled into a graphical conceptual model that indicates the importance of different aspects of giant gartersnake biology for maintaining positive population growth, and identifies those areas for which important information relevant for conservation is lacking. Directing research efforts toward these aspects of giant gartersnake ecology will likely result in improvements to conserving this unique species while meeting the high demands for water in California.

Open-File Report↗

USGS1995

Canada geese in North America

Canada geese ( Branta canadensis ) are probably more abundant now than at any time in history. They rank first among wildlife watchers and second among harvests of waterfowl species in North America. Canada geese are also the most widely distributed and phenotypically (visible characteristics of the birds) variable species of bird in North America. Breeding populations now exist in every province and territory of Canada and in 49 of the 50 United States. The size of the 12 recognized subspecies range from 1.4 kg (3-lb) cackling Canada goose ( B.c. minima ) to the 5.0 kg (11-lb) giant Canada goose ( B.c. maxima ; Delacour 1954; Bellrose 1976). Market hunting and poor stewardship led to record low numbers of geese in the early 1900's, but regulated seasons including closures, refuges, and law enforcement led to restoration of most populations. Winter surveys were begun to study population trends and set responsible harvest regulations for these long-lived and diverse birds. Winter surveys begun in 1936-37 probably represent the oldest continuing index of migratory birds in North America.

Book chapter↗

USGS2006

The importance of diverse data types to calibrate a watershed model of the Trout Lake Basin, Northern Wisconsin, USA

As part of the USGS Water, Energy, and Biogeochemical Budgets project and the NSF Long-Term Ecological Research work, a parameter estimation code was used to calibrate a deterministic groundwater flow model of the Trout Lake Basin in northern Wisconsin. Observations included traditional calibration targets (head, lake stage, and baseflow observations) as well as unconventional targets such as groundwater flows to and from lakes, depth of a lake water plume, and time of travel. The unconventional data types were important for parameter estimation convergence and allowed the development of a more detailed parameterization capable of resolving model objectives with well-constrained parameter values. Independent estimates of groundwater inflow to lakes were most important for constraining lakebed leakance and the depth of the lake water plume was important for determining hydraulic conductivity and conceptual aquifer layering. The most important target overall, however, was a conventional regional baseflow target that led to correct distribution of flow between sub-basins and the regional system during model calibration. The use of an automated parameter estimation code: (1) facilitated the calibration process by providing a quantitative assessment of the model's ability to match disparate observed data types; and (2) allowed assessment of the influence of observed targets on the calibration process. The model calibration required the use of a 'universal' parameter estimation code in order to include all types of observations in the objective function. The methods described in this paper help address issues of watershed complexity and non-uniqueness common to deterministic watershed models. ?? 2005 Elsevier B.V. All rights reserved.

Journal of Hydrology↗

USGS2010

Chemical and textural controls on phosphorus mobility in drylands of southeastern Utah

We investigated several forms of phosphorus (P) in dryland soils to examine the chemical and textural controls on P stabilization on a diverse set of substrates. We examined three P fractions including labile, moderately labile, and occluded as determined by a modified Hedley fractionation technique. The P fractions were compared to texture measurements and total elemental concentrations determined by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). Labile P related to the absence of materials involved in P sorption. Moderately labile P was most strongly associated with high total Al & Fe content that we interpret to represent oxides and 1:1 clay minerals. The occluded P fraction was strongly associated with low total Al & Fe environments and interpreted to represent 2:1 clay minerals where ligand exchange tightly sequesters P. The results indicate that the controls on P fraction distribution are initially closely tied to the chemical and physical properties of the bedrock units that contribute to soil formation. Further, these results suggest that the progression of stabilized P forms in dryland areas differs from the progression observed in mesic environments. Soil development in dryland settings, such as the formation of pedogenic carbonates, may lead to differing controls on P availability and the proportional size of the moderately labile fraction.

Utah↗

USGS2006

Summer food habits and trophic overlap of roundtail chub and creek chub in Muddy Creek, Wyoming

Native fishes of the Upper Colorado River Basin have experienced substantial declines in abundance and distribution, and are extirpated from most of Wyoming. Muddy Creek, in south-central Wyoming (Little Snake River watershed), contains sympatric populations of native roundtail chub (Gila robusta), bluehead sucker, (Catostomus discobolus), and flannelmouth sucker (C. tatipinnis), and represents an area of high conservation concern because it is the only area known to have sympatric populations of all 3 species in Wyoming. However, introduced creek chub (Semotilus atromaculatus) are abundant and might have a negative influence on native fishes. We assessed summer food habits of roundtail chub and creek chub to provide information on the ecology of each species and obtain insight on potential trophic overlap. Roundtail chub and creek chub seemed to be opportunistic generalists that consumed a diverse array of food items. Stomach contents of both species were dominated by plant material, aquatic and terrestrial insects, and Fishes, but also included gastropods and mussels. Stomach contents were similar between species, indicating high trophic, overlap. No length-related patterns in diet were observed for either species. These results suggest that creek chubs have the potential to adversely influence the roundtail chub population through competition for food and the native fish assemblage through predation.

Southwestern Naturalist↗

USGS2020

Flood-frequency estimation for very low annual exceedance probabilities using historical, paleoflood, and regional information with consideration of nonstationarity

Streamflow estimates for floods with an annual exceedance probability of 0.001 or lower are needed to accurately portray risks to critical infrastructure, such as nuclear powerplants and large dams. However, extrapolating flood-frequency curves developed from at-site systematic streamflow records to very low annual exceedance probabilities (less than 0.001) results in large uncertainties in the streamflow estimates. Traditionally, methods for statistically estimating flood frequency have relied on the systematic streamflow record, which provides a time series of annual maximum flood peaks, often including some historical peaks. However, most peak-flow records are less than 100 years, and uncertainties are large when trying to extrapolate magnitudes of very low annual exceedance probability events. Other data may be available that extend the record beyond the systematic dataset. Historical data are defined as data from outside the period of systematic records but within the period of human records. Examples of historical information include flood estimates from other agencies and newspaper accounts that can be translated to flood magnitude point estimates, interval estimates, or perception thresholds (such as a statement that an 1880 flood was the largest since 1869). Paleoflood data, which may also extend the dataset, include a broad range of information about flood occurrence or magnitude from sources like sediment deposits or tree rings. Several assumptions are made in flood-frequency analysis, and an understanding of whether the data conform to these assumptions is desired. A particularly difficult assumption to evaluate for flood-frequency analysis is the underlying assumption that the flood series is stationary—the assumption that a time series of peak flow varies around a constant mean within a particular range of values (constant variance). As the hydrologic community’s understanding of natural systems and anthropogenic effects on streamflows has evolved, the community has come to understand that many surface-water systems exhibit one or more forms of nonstationarity, and thus the stationarity assumption is often violated to some degree. However, there is currently (2020) no consensus among hydrologists regarding the most appropriate flood-frequency-analysis methods for nonstationary systems, and this topic remains an active area of research. A literature review was completed to summarize the state of the science of flood frequency. The literature review highlights tools available to detect nonstationarities and identifies approaches that include external information to inform flood-frequency analysis. To demonstrate methods for initial data analysis and for incorporating historical and paleoflood information in flood-frequency analysis, five sites were selected: the Red River of the North at James Avenue Pumping Station, Winnipeg, Manitoba, Canada; lower reach, Rapid Creek, South Dakota; Spring Creek, South Dakota; Cherry Creek near Melvin, Colorado; and Escalante River near Escalante, Utah. The sites were chosen for the availability of published historical and paleoflood data and for their geographic diversity and unique characteristics, which highlighted issues such as autocorrelation, change points, trends, outlier peaks, or short periods of record. An initial data analysis that involved examining records for autocorrelation, change points, and trends was completed for all sites. The flood-frequency analysis completed for this study used version 7.2 of the U.S. Geological Survey PeakFQ program. Multiple analyses were done on each site documenting the change in the flood-frequency curve when additional historical or paleoflood data were added. When other flood-frequency studies were available, their results were compared to the results here. The comparisons in some cases simply show the effect of additional years of data, whereas other comparisons show results from probability distributions or fitting methods other than those used in PeakFQ. For the Red River of the North, flood-frequency analysis shows that paleoflood data appear necessary to reasonably estimate very low annual exceedance probabilities. For the analysis of the lower reach of Rapid Creek and Spring Creek, paleoflood information helped put a high outlier from the systematic period in context; however, very low annual exceedance probabilities at these sites still had extraordinarily large confidence bounds. These sites also showed that paleoflood information might be transferred from one site to another, with the caveat that this is a case where we had existing paleoflood data to test the transfer of paleoflood information—this is not the case at many sites, and transferring paleoflood information requires assumptions about the comparability of floods at the sites. The Cherry Creek analysis affirmed the result of an earlier study that showed that the generalized Pareto distribution was not a good distribution for estimating very low annual exceedance probabilities. The Escalante River analysis showed that adding paleoflood information might increase uncertainty for very low annual exceedance probabilities, compared to analysis with the systematic period of record information only, when the paleoflood peaks are of much larger magnitudes than the systematic record.

Scientific Investigations Report↗

USGS2026

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish ( C. clupeaformis ) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish ( Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium -specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3,066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.

BioRxiv↗

USGS2024

Prioritizing water availability study settings to address geogenic contaminants and related societal factors

Water availability for human and ecological uses depends on both water quantity and water quality. The U.S. Geological Survey (USGS) is developing strategies for prioritizing regional-scale and watershed basin-scale studies of water availability across the nation. Previous USGS ranking processes for basin-scale studies incorporated primarily water quantity factors but are now considering additional water quality factors. This study presents a ranking based on the potential impacts of geogenic constituents on water quality and consideration of societal factors related to water quality. High-concentration geogenic constituents, including trace elements and radionuclides, are among the most prevalent contaminants limiting water availability in the USA and globally. Geogenic constituents commonly occur in groundwater because of subsurface water–rock interactions, and their distributions are controlled by complex geochemical processes. Geogenic constituent mobility can also be affected by human activities (e.g., mining, energy production, irrigation, and pumping). Societal factors and relations to drinking water sources and water quality information are often overlooked when evaluating research priorities. Sociodemographic characteristics, data gaps resulting from historical data-collection disparities, and infrastructure condition/age are examples of factors to consider regarding environmental justice. This paper presents approaches for ranking and prioritizing potential basin-scale study areas across the contiguous USA by considering a suite of conventional physical and geochemical variables related to geogenic constituents, with and without considering variables related to societal factors. Simultaneous consideration of societal and conventional factors could provide decision makers with more diverse, interdisciplinary tools to increase equity and reduce bias in prioritizing focused research areas and future water availability studies.

Environmental Monitoring and Assessment↗

USGS2013

VisTrails SAHM: visualization and workflow management for species habitat modeling

The Software for Assisted Habitat Modeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre- and post-processing steps and modeling options incorporated in the construction of a species distribution model through the established workflow management and visualization VisTrails software. This paper provides an overview of the VisTrails:SAHM software including a link to the open source code, a table detailing the current SAHM modules, and a simple example modeling an invasive weed species in Rocky Mountain National Park, USA.

Ecography: Pattern and Diversity in Ecology↗

USGS2014

Linking rapid magma reservoir assembly and eruption trigger mechanisms at evolved Yellowstone-type supervolcanoes

The geological record contains evidence of volcanic eruptions that were as much as two orders of magnitude larger than the most voluminous eruption experienced by modern civilizations, the A.D. 1815 Tambora (Indonesia) eruption. Perhaps nowhere on Earth are deposits of such supereruptions more prominent than in the Snake River Plain–Yellowstone Plateau (SRP-YP) volcanic province (northwest United States). While magmatic activity at Yellowstone is still ongoing, the Heise volcanic field in eastern Idaho represents the youngest complete caldera cycle in the SRP-YP, and thus is particularly instructive for current and future volcanic activity at Yellowstone. The Heise caldera cycle culminated 4.5 Ma ago in the eruption of the &sim;1800 km 3 Kilgore Tuff. Accessory zircons in the Kilgore Tuff display significant intercrystalline and intracrystalline oxygen isotopic heterogeneity, and the vast majority are 18 O depleted. This suggests that zircons crystallized from isotopically distinct magma batches that were generated by remelting of subcaldera silicic rocks previously altered by low-δ 18 O meteoric-hydrothermal fluids. Prior to eruption these magma batches were assembled and homogenized into a single voluminous reservoir. U-Pb geochronology of isotopically diverse zircons using chemical abrasion–isotope dilution–thermal ionization mass spectrometry yielded indistinguishable crystallization ages with a weighted mean 206 Pb/ 238 U date of 4.4876 ± 0.0023 Ma (MSWD = 1.5; n = 24). These zircon crystallization ages are also indistinguishable from the sanidine 40 Ar/ 39 Ar dates, and thus zircons crystallized close to eruption. This requires that shallow crustal melting, assembly of isolated batches into a supervolcanic magma reservoir, homogenization, and eruption occurred extremely rapidly, within the resolution of our geochronology (10 3 –10 4 yr). The crystal-scale image of the reservoir configuration, with several isolated magma batches, is very similar to the reservoir configurations inferred from seismic data at active supervolcanoes. The connection of magma batches vertically distributed over several kilometers in the upper crust would cause a substantial increase of buoyancy overpressure, providing an eruption trigger mechanism that is the direct consequence of the reservoir assembly process.

Geology↗

USGS2009

Potential effects of runoff, fluvial sediment, and nutrient discharges on the coral reefs of Puerto Rico

Coral reefs, the foundation and primary structure of many highly productive and diverse tropical marine ecosystems, have been degraded by human activity in much of the earth's tropical oceans. To contribute to improved understanding of this problem, the potential relation between river sediment and nutrient discharges and degradation of coral reefs surrounding Puerto Rico was studied using streamflow, suspended-sediment, and water-quality data. Mean annual runoff for the 8711 km2 island is 911 mm, about 57% of mean annual precipitation (1600 mm). Mean annual suspended-sediment discharge from Puerto Rico to coastal waters is estimated at 2.7-9.0 million metric tonnes. Storm runoff transports a substantial part of sediment: the highest recorded daily sediment discharge is 1-3.6 times the mean annual sediment discharge. Hurricane Georges (1998) distributed an average of 300 mm of rain across the island, equivalent to a volume of about 2.6 billion m3. Runoff of more than 1.0 billion m3 of water and as much as 5 to 10 million metric tonnes of sediment were discharged to the coast and shelf. Nitrogen and phosphorous concentrations in river waters are as much as 10 times the estimated presettlement levels. Fecal coliform and fecal streptococcus concentrations in many Puerto Rico rivers are near or above regulatory limits. Unlike sediment discharges, which are predominantly episodic and intense, river-borne nutrient and fecal discharge is a less-intense but chronic stressor to coral reefs found near the mouths of rivers. Negative effects of riverderived sediment and nutrient discharge on coral reefs are especially pronounced on the north, southwest, and west coasts.

Journal of Coastal Research↗

USGS2021

Development and validation of a spatially-explicit agent-based model for space utilization by African savanna elephants (Loxodonta africana) based on determinants of movement

African elephants (Loxodonta africana) are well-studied and inhabit diverse landscapes that are being transformed by both humans and natural forces. Most tools currently in use are limited in their ability to predict how elephants will respond to novel changes in the environment. Individual-, or agent-based modeling (ABM), may extend current methods in addressing and predicting spatial responses to environmental conditions over time. We developed a spatially explicit agent-based model to simulate elephant space use and validated the model with movement data from elephants in Kruger National Park (KNP) and Chobe National Park (CNP). We simulated movement at an hourly scale, as this scale can reflect switches in elephant behavior due to changes in internal states and short-term responses to the local availability and distribution of critical resources, including forage, water, and shade. Known internal drivers of elephant movement, including perceived temperature and the time since an individual last visited a water source, were linked to the external environment through behavior-based movement rules. Simulations were run on model landscapes representing the wet season and the hot, dry season for both parks. The model outputs, including home range size, daily displacement distance, net displacement distance, and maximum distance traveled from a permanent water source, were evaluated through qualitative and quantitative comparisons to actual elephant movement data from both KNP and CNP. The ABM was successful in reproducing the differences in daily displacements between seasons in each park, and in distances traveled from a permanent water source between parks and seasons. Other movement characteristics, including differences in home range sizes and net daily displacements, were partially reproduced. Out of the all the statistical comparisons made between the empirical and simulated movement patterns, the majority were classified as discrepancies of medium or small effect size. We have shown that a resource-driven model with relatively simple decision rules generates trajectories with movement characteristics that are mostly comparable to those calculated from empirical data. Simulating hourly movement (as our model does) may be useful in predicting how finer-scale patterns of space use, such as those created by foraging movements, are influenced by finer spatio-temporal changes in the environment.

Chobe National Park, Kruger National Park↗

USGS2010

Modelling community dynamics based on species-level abundance models from detection/nondetection data

1. In large‐scale field surveys, a binary recording of each species’ detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species‐, functional group‐, and community‐levels from such binary data. 2. We developed a novel hierarchical multi‐species abundance model based on species‐level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species‐level detection/nondetection is linked to species‐level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9‐year dataset composed of the detection/nondetection of forest birds, at a single post‐fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post‐fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications . Understanding and prediction of large‐scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species‐, functional group‐, and community‐levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance‐based diversity and similarity measures under imperfect detection.

Journal of Applied Ecology↗