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At least 145 records · Page 8Linked to original sources
USGS2024

Utility of an instantaneous salt dilution method for measuring streamflow in headwater streams

Streamflow records are biased toward large streams and rivers, yet small headwater streams are often the focus of ecological research in response to climate change. Conventional flow measurement instruments such as acoustic Doppler velocimeters (ADVs) do not perform well during low-flow conditions in small streams, truncating the development of rating curves during critical baseflow conditions dominated by groundwater inflow. We revisited an instantaneous solute tracer injection method as an alternative to ADVs based on paired measurements to compare their precision, efficiency, and feasibility within headwater streams across a range of flow conditions. We show that the precision of discharge measurements using salt dilution by slug injection and ADV methods were comparable overall, but salt dilution was more precise during the lowest flows and required less time to implement. Often, headwater streams were at or below the depth threshold where ADV measurements could even be attempted and transects were complicated by coarse bed material and cobbles. We discuss the methodological benefits and limitations of salt dilution by slug injection and conclude that the method could facilitate a proliferation of streamflow observation across headwater stream networks that are highly undersampled compared to larger streams.

Virginia↗
USGS2012

Bayesian shared frailty models for regional inference about wildlife survival

One can joke that 'exciting statistics' is an oxymoron, but it is neither a joke nor an exaggeration to say that these are exciting times to be involved in statistical ecology. As Halstead et al. 's (2012) paper nicely exemplifies, recently developed Bayesian analyses can now be used to extract insights from data using techniques that would have been unavailable to the ecological researcher just a decade ago. Some object to this, implying that the subjective priors of the Bayesian approach is the pathway to perdition (e.g. Lele & Dennis, 2009). It is reasonable to ask whether these new approaches are really giving us anything that we could not obtain with traditional tried-and-true frequentist approaches. I believe the answer is a clear yes.

Animal Conservation↗
USGS2025

Integrating theory and empirical patterns: Fish body size distributions, life history traits, and environmental flows in streams

Individual size distributions (ISDs) are prominent in ecological research and may support resource managers with ecosystem-scale objectives. We use a database of individual size measurements for US stream fishes to test for direct and indirect effects of traits, flow regimes, and land use on the interspecific ISD exponent. Path analysis indicates that traits have strong, direct effects on ISD. Flow and land use effects on the exponent are largely indirectly mediated by their influences on species traits. ISD exponents increase (abundances of larger-bodied individuals increase, relative to smaller-bodied) when environments favor higher trophic levels, warmer thermal tolerances, and periodic life histories. Alternatively, ISD exponents decrease in systems that favor opportunistic life histories. Our flexible modeling framework that includes direct and indirect effects of traits, flow regimes, and land use on ISD could be expanded to incorporate additional variables that interact with flow (e.g., temperature and physical habitat) to assess of effects of multiple stressors on aquatic ecosystem functioning.

Science Advances↗
USGS2017

Deleterious effects of net clogging on the quantification of stream drift

Drift studies are central to stream and river ecological research. However, a fundamental aspect of quantifying drift — how net clogging affects the accuracy of results — has been widely ignored. Utilizing approaches from plankton and suspended sediment studies in oceanography and hydrology, we examined the rate and dynamics of net clogging across a range of conditions. We found that nets clog nonlinearly over time and that suspended solid concentrations and net mesh size exerted a strong effect on clogging rates. Critically, net clogging introduced unpredictable biases in resultant data due to the inaccuracies in water volume estimates introduced by progressive clogging. This renders the widespread approach to linearly “correct” for clogging inadequate. Using a meta-analysis of 77 drift studies spanning 25 years, we demonstrate that the detrimental effects of net clogging are routinely unappreciated, even though the results of most of these studies were likely affected by clogging. We close by describing an approach for avoiding net clogging, which will increase the accuracy and reproducibility of results in future freshwater, lotic drift studies.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2006

Improving data analysis in herpetology: Using Akaike's information criterion (AIC) to assess the strength of biological hypotheses

In ecology, researchers frequently use observational studies to explain a given pattern, such as the number of individuals in a habitat patch, with a large number of explanatory (i.e., independent) variables. To elucidate such relationships, ecologists have long relied on hypothesis testing to include or exclude variables in regression models, although the conclusions often depend on the approach used (e.g., forward, backward, stepwise selection). Though better tools have surfaced in the mid 1970's, they are still underutilized in certain fields, particularly in herpetology. This is the case of the Akaike information criterion (AIC) which is remarkably superior in model selection (i.e., variable selection) than hypothesis-based approaches. It is simple to compute and easy to understand, but more importantly, for a given data set, it provides a measure of the strength of evidence for each model that represents a plausible biological hypothesis relative to the entire set of models considered. Using this approach, one can then compute a weighted average of the estimate and standard error for any given variable of interest across all the models considered. This procedure, termed model-averaging or multimodel inference, yields precise and robust estimates. In this paper, I illustrate the use of the AIC in model selection and inference, as well as the interpretation of results analysed in this framework with two real herpetological data sets. The AIC and measures derived from it is should be routinely adopted by herpetologists. ?? Koninklijke Brill NV 2006.

Amphibia-Reptilia↗
USGS2021

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H 2 18 O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO 2 ) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18 O in soil and respired CO 2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

Microbiome↗
USGS2017

Evaluation of harvest and information needs for North American sea ducks

Wildlife managers routinely seek to establish sustainable limits of sport harvest or other regulated forms of take while confronted with considerable uncertainty. A growing body of ecological research focuses on methods to describe and account for uncertainty in management decision-making and to prioritize research and monitoring investments to reduce the most influential uncertainties. We used simulation methods incorporating measures of demographic uncertainty to evaluate risk of overharvest and prioritize information needs for North American sea ducks (Tribe Mergini ). Sea ducks are popular game birds in North America, yet they are poorly monitored and their population dynamics are poorly understood relative to other North American waterfowl. There have been few attempts to assess the sustainability of harvest of North American sea ducks, and no formal harvest strategy exists in the U.S. or Canada to guide management. The popularity of sea duck hunting, extended hunting opportunity for some populations (i.e., special seasons and/or bag limits), and population declines have led to concern about potential overharvest. We used Monte Carlo simulation to contrast estimates of allowable harvest and observed harvest and assess risk of overharvest for 7 populations of North American sea ducks: the American subspecies of common eider ( Somateria mollissima dresseri ), eastern and western populations of black scoter ( Melanitta americana ) and surf scoter ( M . perspicillata ), and continental populations of white-winged scoter ( M . fusca ) and long-tailed duck ( Clangula hyemalis ). We combined information from empirical studies and the opinions of experts through formal elicitation to create probability distributions reflecting uncertainty in the individual demographic parameters used in this assessment. Estimates of maximum growth ( r max ), and therefore of allowable harvest, were highly uncertain for all populations. Long-tailed duck and American common eider appeared to be at high risk of overharvest (i.e., observed harvest < allowable harvest in 5–7% and 19–26% of simulations, respectively depending on the functional form of density dependence), whereas the other populations appeared to be at moderate risk to low risk (observed harvest < allowable harvest in 22–68% of simulations, again conditional on the form of density dependence). We also evaluated the sensitivity of the difference between allowable and observed harvest estimates to uncertainty in individual demographic parameters to prioritize information needs. We found that uncertainty in overall fecundity had more influence on comparisons of allowable and observed harvest than adult survival or observed harvest for all species except long-tailed duck. Although adult survival was characterized by less uncertainty than individual components of fecundity, it was identified as a high priority information need given the sensitivity of growth rate and allowable harvest to this parameter. Uncertainty about population size was influential in the comparison of observed and allowable harvest for 5 of the 6 populations where it factored into the assessment. While this assessment highlights a high degree of uncertainty in allowable harvest, it provides a framework for integration of improved data from future research and monitoring. It could also serve as the basis for harvest strategy development as management objectives and regulatory alternatives are specified by the management community.

PLoS ONE↗
USGS2020

The relationship between biodiversity and wetland cover varies across regions of the conterminous United States

Identifying the factors that determine the spatial distribution of biodiversity is a major focus of ecological research. These factors vary with scale from interspecific interactions to global climatic cycles. Wetlands are important biodiversity hotspots and contributors of ecosystem services, but the association between proportional wetland cover and species richness has shown mixed results. It is not well known as to what extent there is a relationship between proportional wetland cover and species richness, especially at the sub-continental scale. We used the National Wetlands Inventory to model wetland cover for the conterminous United States and the National Land Cover Database to estimate wetland change between 2001 and 2011. We used a Bayesian spatial Poisson model to estimate a spatially varying coefficient surface describing the effect of proportional wetland cover on the distribution of amphibians, birds, mammals, and reptiles and the cumulative distribution of terrestrial endemic species. Species richness and wetland cover were significantly correlated, and this relationship varied both spatially and by taxonomic group. Rather than a continental-scale association, however, we found that this relationship changed more closely among ecoregions. The species richness of each of the five groups was positively associated with wetland cover in some or all of the Great Plains; additionally, a positive association was found for mammals in the Southeastern Plains and Piedmont of the eastern U.S. Model results indicated negative association especially in the Cold Deserts and Northern Lakes & Forests of Minnesota and Wisconsin, though these varied greatly between groups. Our results highlight the need for wetland conservation initiatives that focus efforts at the level II and III ecoregional scale rather than along political boundaries.

PLoS ONE↗
USGS2013

The overlooked terrestrial impacts of mountaintop mining

Ecological research on mountaintop mining has been focused on aquatic impacts because the overburden (i.e., the mountaintop) is disposed of in nearby valleys, which leads to a wide range of water-quality impacts on streams. There are also numerous impacts on the terrestrial environment from mountaintop mining that have been largely overlooked, even though they are no less wide ranging, severe, and multifaceted. We review the impacts of mountaintop mining on the terrestrial environment by exploring six broad themes: (1) the loss of topographic complexity, (2) forest loss and fragmentation, (3) forest succession and soil loss, (4) forest loss and carbon sequestration, (5) biodiversity, and (6) human health and well-being.

BioScience↗
USGS2011

Unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance

Ecological research uses data collection techniques that are prone to substantial and unique types of measurement error to address scientific questions about species abundance and distribution. These data collection schemes include a number of survey methods in which unmarked individuals are counted, or determined to be present, at spatially- referenced sites. Examples include site occupancy sampling, repeated counts, distance sampling, removal sampling, and double observer sampling. To appropriately analyze these data, hierarchical models have been developed to separately model explanatory variables of both a latent abundance or occurrence process and a conditional detection process. Because these models have a straightforward interpretation paralleling mechanisms under which the data arose, they have recently gained immense popularity. The common hierarchical structure of these models is well-suited for a unified modeling interface. The R package unmarked provides such a unified modeling framework, including tools for data exploration, model fitting, model criticism, post-hoc analysis, and model comparison.

Journal of Statistical Software↗
USGS2005

Estimating site occupancy and abundance using indirect detection indices

Knowledge of factors influencing animal distribution and abundance is essential in many areas of ecological research, management, and policy-making. Because common methods for modeling and estimating abundance (e.g., capture–recapture, distance sampling) are sometimes not practical for large areas or elusive species, indices are sometimes used as surrogate measures of abundance. We present an extension of the Royle and Nichols (2003) generalization of the MacKenzie et al. (2002) site-occupancy model that incorporates length of the sampling interval into the model for detection probability. As a result, we obtain a modeling framework that shows how useful information can be extracted from a class of index methods we call indirect detection indices (IDIs). Examples of IDIs include scent station, tracking tube, snow track, tracking plate, and hair snare surveys. Our model is maximum likelihood, and it can be used to estimate site occupancy and model factors influencing patterns of occupancy and abundance in space. Under certain circumstances, it can also be used to estimate abundance. We evaluated model properties using Monte Carlo simulations and illustrate the method with tracking tube and scent station data. We believe this model will be a useful tool for determining factors that influence animal distribution and abundance.

Journal of Wildlife Management↗
USGS2005

Early chromite mining and agricultural clearance: Opportunities for the investigation of agricultural sediment dynamics in the Eastern Piedmont (USA)

Many flood plains in the Eastern Piedmont (USA) are buried under deposits of sediment resulting from European agricultural clearance. Classic radioisotopic dating techniques cover temporal periods too short (137Cs, 210Pb) or too long (14C) to reliably date sediments deposited during periods of local European activity (1660-1900). Moreover, many potential biomarkers, such as pollen, degrade in oxic flood plain sediments. In the Baltimore, Maryland (USA) region, early chromite mining (1820 - 1880) occurred during periods of rapid agricultural clearance. Use of chromium (Cr) chemostratigraphic profiles in flood plain sediments tied to historical mining activity can provide improved precision in overbank accumulation rates and timing. Sediment cores were collected from the Red Run basin, which is part of the Baltimore Ecosystem Study, an urban Long-Term Ecological Research site. Trace metal chemostratigraphic profiles were measured and peaks in Cr concentration tied to historic mining activity. Dates from Cr chemostratigraphic profiles were combined with 137Cs dating to reconstruct flood plain sedimentation rates. Red Run early sedimentation rates (1820 - 1880) were higher (0.45 - 1.19 cm/yr) than more recent (1880 - 1963) rates (0.08 - 0.46 cm/yr). This indicates that Piedmont flood plain vertical sediment accumulation might have peaked before the peak in agricultural clearance, earlier than assumed by regional models. The Cr chemostratigraphy is applicable to a wider region including much of the Maryland and Pennsylvania (USA) Piedmont.

American Journal of Science↗
USGS2007

Landscape ecology

Over the next few years, the Leetown Science Center (LSC) would like to establish an expanded capability for conducting landscape ecology research.

Fact Sheet↗
USGS2022

Abundance and productivity of Marbled Murrelets ( Brachyramphus marmoratus ) off central California during the 2020 and 2021 breeding seasons

Marbled murrelets ( Brachyramphus marmoratus ) have been listed as “endangered” by the State of California and “threatened” by the U.S. Fish and Wildlife Service since 1992 in California, Oregon, and Washington. Information regarding marbled murrelet abundance, distribution, population trends, and habitat associations is critical for risk assessment, effective management, evaluation of conservation efficacy, and ultimately, to meet federal- and state-mandated recovery efforts for this species. During June–August 2020 and 2021, the U.S. Geological Survey Western Ecological Research Center continued previously established, long-term (1999–present), at-sea surveys to estimate abundance and productivity of marbled murrelets in U.S. Fish and Wildlife Service Conservation Zone 6 (San Francisco Bay to Point Sur in central California). The abundance estimated for the entire study area was 470 birds (95-percent confidence interval, 313–707 birds) in 2020 and 402 birds (95-percent confidence interval, 219–737 birds) in 2021. Estimated abundances for both years are comparable with most prior years of study. We estimated reproductive productivity (calculated as the hatch-year to after-hatch-year ratio) after date-correcting hatch-year and after-hatch-year counts to account for birds expected to be absent from the water while inland at nests. The date-corrected juvenile ratio was 0.018±0.011 standard error in 2020 and 0.041±0.024 standard error in 2021. We updated a comprehensive database of all Zone 6 marbled murrelet survey data since 1999 with 2020–21 data to allow scientists and managers to evaluate established survey methods and assess trends in abundance and productivity estimates.

California↗
USGS2018

Abundance and productivity of marbled murrelets (Brachyramphus marmoratus) off central California during the 2017 breeding season

Marbled murrelets ( Brachyramphus marmoratus ) have been listed as “Endangered” by the State of California and “Threatened” by the U.S. Fish and Wildlife Service since 1992 in California, Oregon, and Washington. Information regarding marbled murrelet abundance, distribution, population trends, and habitat associations is critical for risk assessment, effective management and evaluation of conservation efficacy, and ultimately to meet Federal- and State-mandated recovery efforts for this species. During June–August 2017, the U.S. Geological Survey Western Ecological Research Center continued previously established, long-term (1999–2016), at-sea surveys to estimate abundance and productivity of marbled murrelets in U.S. Fish and Wildlife Service Conservation Zone 6 (central California—San Francisco Bay to Monterey Bay). Using conventional distance sampling methods, we estimated marbled murrelet abundance using 189 detections of 321 individuals observed on nine unique surveys. The abundance estimated for the entire study area using all surveys in 2017 was 530 birds (95-percent confidence interval, 384–732 birds). Estimated abundance from 2017 is comparable to most prior years of study, except for 2008 and 2015, which had anomalously low abundances. We estimated productivity (calculated as the hatch-year [HY] to after-hatch-year [AHY] ratio) in 2017 using three detections of three individuals observed in six surveys. After date-correcting HY and AHY counts to account for birds expected to be absent from the water while inland at nests, the date-corrected juvenile ratio was 0.022 ± 0.014 standard error. We created a synthesized database of all marbled murrelet survey data from 1999 to 2017 to allow scientists and managers to evaluate established survey methods and assess trends in abundance and productivity estimates. Future modifications of survey design could help reduce variance in abundance estimation.

California↗
USGS2019

Abundance and productivity of marbled murrelets (Brachyramphus marmoratus) off central California during the 2018 breeding season

Executive Summary Marbled murrelets ( Brachyramphus marmoratus ) have been listed as “endangered” by the State of California and “threatened” by the U.S. Fish and Wildlife Service since 1992 in California, Oregon, and Washington. Information regarding marbled murrelet abundance, distribution, population trends, and habitat associations is critical for risk assessment, effective management, evaluation of conservation efficacy, and ultimately, to meet Federal- and State-mandated recovery efforts for this species. During June–August 2018, the U.S. Geological Survey Western Ecological Research Center continued previously established, long-term (1999–2018), at-sea surveys to estimate abundance and productivity of marbled murrelets in U.S. Fish and Wildlife Service Conservation Zone 6 (San Francisco Bay to Point Sur in central California). Using conventional distance sampling methods, we estimated marbled murrelet abundance using 137 detections of 227 individuals observed on 9 surveys. The abundance estimated for the entire study area using all surveys in 2018 was 370 birds (95-percent confidence interval, 250–546 birds). Estimated abundance from 2018 is comparable to most prior years of study, except for 2001–03, when greater abundances were estimated. In 2018, we estimated reproductive productivity (calculated as the hatch-year [HY] to after-hatch-year [AHY] ratio) using four detections of four HY individuals observed on six surveys. After date-correcting HY and AHY counts to account for birds expected to be absent from the water while inland at nests, the date-corrected juvenile ratio was 0.047 ± 0.024 standard error. We updated a synthesized database of all Zone 6 marbled murrelet survey data since 1999 with 2018 data to allow scientists and managers to evaluate established survey methods and assess trends in abundance and productivity estimates.

California↗
USGS2020

Abundance and productivity of marbled murrelets ( Brachyramphus marmoratus ) off central California during the 2019 breeding season

Marbled murrelets ( Brachyramphus marmoratus ) have been listed as “endangered” by the State of California and “threatened” by the U.S. Fish and Wildlife Service since 1992 in California, Oregon, and Washington. Information regarding marbled murrelet abundance, distribution, population trends, and habitat associations is critical for risk assessment, effective management, evaluation of conservation efficacy, and ultimately, to meet Federal and State recovery efforts for this species. During June–August 2019, the U.S. Geological Survey Western Ecological Research Center continued previously established, long-term (1996–2019), at-sea surveys to estimate abundance and productivity of marbled murrelets in U.S. Fish and Wildlife Service Conservation Zone 6 (San Francisco Bay to Point Sur in central California). Using conventional distance sampling methods, we estimated marbled murrelet abundance using 125 detections of 216 murrelets (mean group size, 1.72) observed on 8 surveys. The abundance estimated for the entire study area using all surveys in 2019 was 404 birds (95-percent confidence interval, 272–601 birds). Estimated abundance from 2019 is comparable to most prior years of study. In 2019, we estimated reproductive productivity (calculated as the hatch-year [HY] to after-hatch-year [AHY] ratio) using three detections of three HY murrelets observed on six surveys. After date-correcting HY and AHY counts to account for birds expected to be absent from the water while inland at nests, the date-corrected juvenile ratio was 0.025±0.020 standard error. We discuss changes in methodologies during 1996–2019 that could be addressed in re-analysis of this long-term dataset. We updated a synthesized database of all Zone 6 marbled murrelet survey data since 1999 with 2019 data to allow scientists and managers to evaluate established survey methods and assess trends in abundance and productivity estimates.

California↗
USGS2009

U.S. Geological Survey (USGS) Western Region: Seabirds coastal and ocean science

From the cold, high Arctic area of Alaska to the warm, tropical Pacific area of Hawai'i, a diverse array of seabird species numbering in the millions of individuals live off the bounty of the Pacific Ocean. Many come to land only to nest and raise their young - these are species supremely adapted for life on the water, whether it be near the coast or hundreds of miles at sea. Those seabirds that reside in the North Pacific year-round are joined each summer by millions of migrant birds that leave the southern hemisphere in winter for better feeding conditions in the north. Seabirds in the Pacific remain one of the great wildlife spectacles on the earth. Yet, seabirds face a number of threats such as oil spills, introduction of predators to their nesting islands, and conflicts with fisheries. State and Federal agencies require increasingly sophisticated information on population dynamics, breeding biology, and feeding ecology to successfully manage these species and their ecosystems. Within the Western Region of the USGS, scientists from the Alaska Science Center (ASC), Western Ecological Research Center (WERC), and Pacific Islands Ecosystems Research Center are leading the way in conducting research on many of these little known species. Their aim is to improve our understanding of seabirds in the Pacific and to provide information to support informed management of the birds and their ecosystems.

Fact Sheet↗