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At least 757 records · Page 42Linked to original sources

USGS2018

Range expansion in unfavorable environments through behavioral responses to microclimatic conditions: Moose (Alces americanus) as the model

Wildlife populations occurring at the edge of their range boundaries are thought to be the most sensitive to climate change due to temperatures being at or near the limit of a species’ thermal envelope. Moose ( Alces americanus ) are a cold adapted species that are showing population declines in some portions of the southern edge of their range. However, other moose populations are actively expanding southward into thermally stressful areas. The direct effects of temperature on moose have not yet been studied in these southwardly expanding populations and may offer insights into how moose are successfully establishing in areas at the edge of their thermal envelope. We used ambient temperature and GPScollar data from moose to quantify the direct effect of temperature on moose habitat use in Massachusetts, USA, which is one of these southwardly expanding populations. The mean daily temperature in our study area exceeded the reported physiological tolerances of moose in over 90% of daytime and 75% of nighttime locations in summer and in over 80% of daytime and 67% of nighttime locations in winter. Across seasons and times of day, moose preferred regenerating forest, but as ambient air temperatures increased, selection for regenerating forest declined and selection for forested wetlands and coniferous forestincreased. This response indicates moose are altering their behavior to utilize thermal shelters when temperatures are high. We observed higher temperatures and stronger behavioral responses than other studies at the southern edge of moose range. We found habitat for moose in Massachusetts is climatically marginal and loss of habitat, increase in parasites, and further climatic warming may cause population declines in the future.

Mammalian Biology↗

USGS2014

Long-term growth-increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth-increment width chronologies for freshwater mussel species in the Pacific Northwest, United States and integrate them with tree-ring data to evaluate how terrestrial and aquatic indicators respond to hydroclimatic variability, including river discharge and precipitation. Annual discharge averaged across water years (October 1–September 30) was highly synchronous among river systems and imparted a coherent pattern among mussel chronologies. The leading principal component of the five longest mussel chronologies (1982–2003; PC1 mussel ) accounted for 47% of the dataset variability and negatively correlated with the leading principal component of river discharge (PC1 discharge ; r = −0.88; P < 0.0001). PC1 mussel and PC1 discharge were closely linked to regional wintertime precipitation patterns across the Pacific Northwest, the season in which the vast majority of annual precipitation arrives. Mussel growth was also indirectly related to tree radial growth, though the nature of the relationships varied across the landscape. Negative correlations occurred in forests where tree growth tends to be limited by drought while positive correlations occurred in forests where tree growth tends to be limited by deep or lingering snowpack. Overall, this diverse assemblage of chronologies illustrates the importance of winter precipitation to terrestrial and freshwater ecosystems and suggests that a complexity of climate responses must be considered when estimating the biological impacts of climate variability and change.

Idaho, Oregon, Washington↗

USGS2012

Emerging prion disease drives host selection in a wildlife population

Infectious diseases are increasingly recognized as an important force driving population dynamics, conservation biology, and natural selection in wildlife populations. Infectious agents have been implicated in the decline of small or endangered populations and may act to constrain population size, distribution, growth rates, or migration patterns. Further, diseases may provide selective pressures that shape the genetic diversity of populations or species. Thus, understanding disease dynamics and selective pressures from pathogens is crucial to understanding population processes, managing wildlife diseases, and conserving biological diversity. There is ample evidence that variation in the prion protein gene (PRNP) impacts host susceptibility to prion diseases. Still, little is known about how genetic differences might influence natural selection within wildlife populations. Here we link genetic variation with differential susceptibility of white-tailed deer to chronic wasting disease (CWD), with implications for fitness and disease-driven genetic selection. We developed a single nucleotide polymorphism (SNP) assay to efficiently genotype deer at the locus of interest (in the 96th codon of the PRNP gene). Then, using a Bayesian modeling approach, we found that the more susceptible genotype had over four times greater risk of CWD infection; and, once infected, deer with the resistant genotype survived 49% longer (8.25 more months). We used these epidemiological parameters in a multi-stage population matrix model to evaluate relative fitness based on genotype-specific population growth rates. The differences in disease infection and mortality rates allowed genetically resistant deer to achieve higher population growth and obtain a long-term fitness advantage, which translated into a selection coefficient of over 1% favoring the CWD-resistant genotype. This selective pressure suggests that the resistant allele could become dominant in the population within an evolutionarily short time frame. Our work provides a rare example of a quantifiable disease-driven selection process in a wildlife population, demonstrating the potential for infectious diseases to alter host populations. This will have direct bearing on the epidemiology, dynamics, and future trends in CWD transmission and spread. Understanding genotype-specific epidemiology will improve predictive models and inform management strategies for CWD-affected cervid populations.

Ecological Applications↗

USGS2010

Inter-regional comparison of land-use effects on stream metabolism

1. Rates of whole-system metabolism (production and respiration) are fundamental indicators of ecosystem structure and function. Although first-order, proximal controls are well understood, assessments of the interactions between proximal controls and distal controls, such as land use and geographic region, are lacking. Thus, the influence of land use on stream metabolism across geographic regions is unknown. Further, there is limited understanding of how land use may alter variability in ecosystem metabolism across regions.2. Stream metabolism was measured in nine streams in each of eight regions (n = 72) across the United States and Puerto Rico. In each region, three streams were selected from a range of three land uses: agriculturally influenced, urban-influenced, and reference streams. Stream metabolism was estimated from diel changes in dissolved oxygen concentrations in each stream reach with correction for reaeration and groundwater input.3. Gross primary production (GPP) was highest in regions with little riparian vegetation (sagebrush steppe in Wyoming, desert shrub in Arizona/New Mexico) and lowest in forested regions (North Carolina, Oregon). In contrast, ecosystem respiration (ER) varied both within and among regions. Reference streams had significantly lower rates of GPP than urban or agriculturally influenced streams.4. GPP was positively correlated with photosynthetically active radiation and autotrophic biomass. Multiple regression models compared using Akaike's information criterion (AIC) indicated GPP increased with water column ammonium and the fraction of the catchment in urban and reference land-use categories. Multiple regression models also identified velocity, temperature, nitrate, ammonium, dissolved organic carbon, GPP, coarse benthic organic matter, fine benthic organic matter and the fraction of all land-use categories in the catchment as regulators of ER.5. Structural equation modelling indicated significant distal as well as proximal control pathways including a direct effect of land-use on GPP as well as SRP, DIN, and PAR effects on GPP; GPP effects on autotrophic biomass, organic matter, and ER; and organic matter effects on ER.6. Overall, consideration of the data separated by land-use categories showed reduced inter-regional variability in rates of metabolism, indicating that the influence of agricultural and urban land use can obscure regional differences in stream metabolism. ?? 2010 Blackwell Publishing Ltd.

Freshwater Biology↗

USGS2003

Combining inferences from models of capture efficiency, detectability, and suitable habitat to classify landscapes for conservation of threatened bull trout

Effective conservation efforts for at-risk species require knowledge of the locations of existing populations. Species presence can be estimated directly by conducting field-sampling surveys or alternatively by developing predictive models . Direct surveys can be expensive and inefficient, particularly for rare and difficult-to-sample species, and models of species presence may produce biased predictions. We present a Bayesian approach that combines sampling and model -based inferences for estimating species presence. The accuracy and cost-effectiveness of this approach were compared to those of sampling surveys and predictive models for estimating the presence of the threatened bull trout (Salvelinus confluentus) via simulation with existing models and empirical sampling data. Simulations indicated that a sampling-only approach would be the most effective and would result in the lowest presence and absence misclassification error rates for three thresholds of detection probability. When sampling effort was considered, however, the combined approach resulted in the lowest error rates per unit of sampling effort. Hence, lower probability-of-detection thresholds can be specified with the combined approach, resulting in lower misclassification error rates and improved cost-effectiveness.

Conservation Biology↗

USGS2016

Rapid carbon loss and slow recovery following permafrost thaw in boreal peatlands

Permafrost peatlands store one-third of the total carbon (C) in the atmosphere and are increasingly vulnerable to thaw as high-latitude temperatures warm. Large uncertainties remain about C dynamics following permafrost thaw in boreal peatlands. We used a chronosequence approach to measure C stocks in forested permafrost plateaus (forest) and thawed permafrost bogs, ranging in thaw age from young (<10 years) to old (>100 years) from two interior Alaska chronosequences. Permafrost originally aggraded simultaneously with peat accumulation (syngenetic permafrost) at both sites. We found that upon thaw, C loss of the forest peat C is equivalent to ~30% of the initial forest C stock and is directly proportional to the prethaw C stocks. Our model results indicate that permafrost thaw turned these peatlands into net C sources to the atmosphere for a decade following thaw, after which post-thaw bog peat accumulation returned sites to net C sinks. It can take multiple centuries to millennia for a site to recover its prethaw C stocks; the amount of time needed for them to regain their prethaw C stocks is governed by the amount of C that accumulated prior to thaw. Consequently, these findings show that older peatlands will take longer to recover prethaw C stocks, whereas younger peatlands will exceed prethaw stocks in a matter of centuries. We conclude that the loss of sporadic and discontinuous permafrost by 2100 could result in a loss of up to 24 Pg of deep C from permafrost peatlands.

Global Change Biology↗

USGS2023

Quantifying uncertainty in coastal salinity regime for biological application using quantile regression

Salinity regimes in coastal ecosystems are highly dynamic and driven by complex geomorphic and hydrological processes. Estuarine biota are generally adapted to salinity fluctuation, but are vulnerable to salinity extremes. Characterizing coastal salinity regime for ecological studies therefore requires representing extremes of salinity ranges at time scales relevant to ecology (e.g., daily, monthly, and seasonally). Here, we propose a framework for modeling coastal salinity with these overall goals: (1) quantify uncertainty in salinity associated with important terrestrial and oceanographic drivers, (2) examine time scales of salinity response to river streamflow events, and (3) predict salinity continuously over space at key time scales. Salinity is modeled as quantile surfaces related to river discharge, tidal dynamics, wind, and spatial location, applied to Suwannee Sound estuary, FL, USA, where salinity has been monitored spatially since 1981. Each quantile level is regressed independently, and together they comprise a distribution of salinity uncertainty across space, with upper and lower quantiles describing salinity extremes. Effects of physical drivers on salinity are compared through four base models with various combinations of tide and wind variables, each including spatial coordinates and a single streamflow metric (in cubic meters per second). Multiple time scales of streamflow are considered by taking means across various periods, from 1 to 12 days, and at various lagged intervals prior to salinity sample, totaling 144 streamflow metrics. We found that the Suwannee coastal salinity regime is dynamic at multiple time scales and varies nonlinearly across space from the river effluence outward. Salinity increases nonlinearly with decreasing river flow rates below 200 m 3 /s, most prominently in the lower quantiles of salinity (τ = 0.05–0.25). Wind appears to have a stronger influence on salinity than astronomic tides for this estuary. The regression approach developed here can be applied to any coastal system that has sufficient spatial and temporal monitoring coverage to capture multiple flood and drought events. It is implemented with a simple R routine, and is less computationally-intensive than finite difference hydrodynamic modeling. The characterizations of salinity uncertainty developed in these analyses can be directly applied to future studies of fish and wildlife responses to changes in watershed management.

Florida↗

USGS1998

Natural attenuation of chlorinated-hydrocarbon contamination at Fort Wainwright, Alaska: A hydrogeochemical and microbiological investigation workplan

Natural attenuation processes include biological degradation, by which microorganisms break down contaminants into simpler product compounds; adsorption of contaminants to soil particles, which decreases the mass of contaminants dissolved in ground water; and dispersion, which decreases dissolved contaminant concentrations through dilution. The primary objectives of this study are to (1) assess the degree to which such natural processes are attenuating chlorinated-hydrocarbon contamination in ground water, and (2) evaluate the effects of ground-water/surface-water interactions on natural-attenuation processes in the area of the former East and West Quartermasters Fueling Systems for Fort Wainwright, Alaska. The study will include investigations of the hydrologic, geochemical, and microbiological processes occurring at this site that influence the transport and fate of chlorinated hydrocarbons in ground water. To accomplish these objectives, a data-collection program has been initiated that includes measurements of water-table elevations and the stage of the Chena River; measurements of vertical temperature profiles within the subsurface; characterization of moisture distribution and movement in the unsaturated zone; collection of ground-water samples for determination of both organic and inorganic chemical constituents; and collection of ground-water samples for enumeration of microorganisms and determination of their potential to mineralize contaminants. We will use results from the data-collection program described above to refine our conceptual model of hydrology and contaminant attenuation at this site. Measurements of water-table elevations and river stage will help us to understand the magnitude and direction of ground-water flow and how changes in the stage of the Chena River affect ground-water flow. Because ambient ground water and surface water typically have different temperature characteristics, temperature monitoring will likely provide further insight into ground-water/surface-water interactions in the subsurface. Characterization of the unsaturated zone will improve our understanding of interactions among ground water, the unsaturated zone, and the atmosphere. The interactions likely of importance to this study include the migration of water, dissolved contaminants, nutrients, and gases (oxygen, carbon dioxide, and methane) between the saturated and unsaturated zones. We will use the results of ground-water chemical analyses to determine the spatial and temporal distribution of (1) chlorinated-hydrocarbon contaminants and their degradation products, (2) oxidation-reduction indicators, (3) nutrients, and (4) major ground-water ions. These water-quality data will provide insight into ground-water flow directions, interactions between ground water and surface water, attenuation of contaminant concentrations caused by dispersion, and intrinsic microbiological processes. Microbiological analyses will indicate whether microorganisms at the site are capable of degrading the contaminants of interest, and will allow us to estimate their potential to attenuate existing contamination. Physical and chemical data interpreted as part of the analysis of ground water and surface water mixing will improve our understanding of the relationship between water quality and contaminant source mixing.

Alaska↗

USGS1998

Water-quality assessment of the lower Illinois River Basin: Environmental setting

The lower Illinois River Basin (LIRB) encompasses 18,000 square miles of central and western Illinois. Historical and recent information from Federal, State, and local agencies describing the physiography, population, land use, soils, climate, geology, streamflow, habitat, ground water, water use, and aquatic biology is summarized to describe the environmental setting of the LIRB. The LIRB is in the Till Plains Section of the Central Lowland physiographic province. The basin is characterized by flat topography, which is dissected by the Illinois River. The drainage pattern of the LIRB has been shaped by many bedrock and glacial geologic processes. Erosion prior to and during Pleistocene time created wide and deep bedrock valleys. The thickest deposits and most major aquifers are in buried bedrock valleys. The Wisconsinan glaciation, which bisects the northern half of the LIRB, affects the distribution and characteristics of glacial deposits in the basin. Agriculture is the largest land use and forested land is the second largest land use in the LIRB. The major urban areas are near Peoria, Springfield, Decatur, and Bloomington-Normal. Soil type and distribution affect the amount of soil erosion, which results in sedimentation of lakes and reservoirs in the basin. Rates of soil erosion of up to 2 percent per year of farmland soil have been measured. Many of the 300 reservoirs, lakes, and wetlands are disappearing because of sedimentation resulting from agriculture activities, levee building, and urbanization. Sedimentation and the destruction of habitat appreciably affect the ecosystem. The Illinois River is a large river-floodplain ecosystem where biological productivity is enhanced by annual flood pulses that advance and retreat over the flood plain and temporarily expand backwater and flood-plain lakes. Ground-water discharge to streams affects the flow and water quality of the streams. The water budget of several subbasins show variability in ground-water contribution from runoff and storage. More than half of the drinking water, including domestic and public-supply use, in the LIRB is from ground water. Fifty-two percent of the public-supply water is from surface water. Ground-water withdrawals mostly are from glacial sand and gravel aquifers. Structural features, such as monoclines, synclines, and anticlines, in the buried bedrock affect the water quality of the aquifers. There are five natural environmental divisions in the LIRB. The Grand Prairie covers most of the northeastern half of the basin, and the Western Forest-Prairie covers most of the southwestern half. Implications of environmental setting for water quality in the LIRB are related primarily to land use. The balanced fish community indicates that the lower Illinois River is affected less from urban and industrial waste than the upper Illinois River. A decrease in dissolved oxygen concentrations and turbidity in the lower reaches of the basin in 1993 have resulted from the recent influx of European zebra mussels to the LIRB. Many factors affect water quality in the LIRB. Bedrock and surface topography, type of glacial material, and land use most directly affect water quality in the basin.

Illinois↗

USGS2014

Tracking geomorphic signatures of watershed suburbanization with multi-temporal LiDAR

Urban development practices redistribute surface materials through filling, grading, and terracing, causing drastic changes to the geomorphic organization of the landscape. Many studies document the hydrologic, biologic, or geomorphic consequences of urbanization using space-for-time comparisons of disparate urban and rural landscapes. However, no previous studies have documented geomorphic changes from development using multiple dates of high-resolution topographic data at the watershed scale. This study utilized a time series of five sequential light detection and ranging (LiDAR) derived digital elevation models (DEMs) to track watershed geomorphic changes within two watersheds throughout development (2002–2008) and across multiple spatial scales (0.01–1 km 2 ). Development-induced changes were compared against an undeveloped forested watershed during the same time period. Changes in elevations, slopes, hypsometry, and surface flow pathways were tracked throughout the development process to assess watershed geomorphic alterations. Results suggest that development produced an increase in sharp topographic breaks between relatively flat surfaces and steep slopes, replacing smoothly varying hillslopes and leading to greater variation in slopes. Examinations of flowpath distributions highlight systematic modifications that favor rapid convergence in unchanneled upland areas. Evidence of channel additions in the form of engineered surface conduits is apparent in comparisons of pre- and post-development stream maps. These results suggest that topographic modification, in addition to impervious surfaces, contributes to altered hydrologic dynamics observed in urban systems. This work highlights important considerations for the use of repeat LiDAR flights in analyzing watershed change through time. Novel methods introduced here may allow improved understanding and targeted mitigation of the processes driving geomorphic changes during development and help guide future research directions for development-based watershed studies.

Geomorphology↗

USGS2020

Freshwater crabs (Decapoda: Pseudothelphusidae) increase rates of leaf breakdown in a neotropical headwater stream

Freshwater crabs are the largest macroconsumers in many neotropical headwater streams, but few studies have examined their roles in ecosystem processes such as leaf litter breakdown. As omnivorous macroconsumers, freshwater crabs affect multiple trophic levels. They may directly increase leaf breakdown through fragmentation and consumption or indirectly decrease breakdown by consuming other macroinvertebrates, including shredders and detritivores. In a headwater stream in Monteverde, Costa Rica, we conducted an in‐stream experiment with 40 enclosures to quantify the effects of pseudothelphusid crabs on both leaf breakdown and macroinvertebrate colonisation of leaves. Half of the enclosures were randomly selected to contain two crabs (mean carapace width = 30 mm) and half were controls without crabs. We sampled mixed leaf packs from the enclosures on days 11, 19, 28, 34, and 42. We found the leaves of one species ( Koanophyllon pittieri ) almost completely decomposed by day 28 in both treatments (crab versus no crab). The other two leaf species ( Meliosma idiopoda , Quercus brenesii ) composed the remaining leaf mass at the end of the experiment. At 42 days, enclosures with crabs had faster rates of leaf breakdown than those without crabs (with crabs: k = −0.020; without crabs: k = −0.016; p = 0.034). This suggests that the magnitude of direct leaf breakdown by crabs, due to fragmentation, consumption, or manipulation of leaves, was greater than any indirect effects on leaf breakdown via crab consumption of other leaf‐consuming species. Macroinvertebrate composition based on taxa abundances or biomasses did not significantly differ between treatments (ANOSIM; p = 0.73 and p = 0.65, respectively). Shredder and detritivore abundances and biomasses increased significantly through time (ANOVA; p ≤ 0.001), but there was no evidence of an effect of crab presence ( p > 0.2), nor were there significant interactions between crab presence and time ( p > 0.3). This is one of the first studies to quantify the effects of pseudothelphusid freshwater crabs on leaf breakdown rates. Our results suggest that these crabs can play a significant role in detrital processing in neotropical headwater streams. This study has also demonstrated that short‐term enclosure experiments are useful in measuring in‐stream effects of crab activity on leaf breakdown.

Quebrada Máquina↗

USGS2022

Ingested toxicity of antimycin A to grass carp Ctenopharyngodon idella and black carp Mylopharyngodon piceus in two carriers

Toxic baits are a potential control mechanism for nuisance carps, but rotenone-based baits for grass carp Ctenopharyngodon idella have been ineffective. Failures have been attributed to the palatability of rotenone because innocuous training pellets are readily consumed prior to provision of piscicide baits. Several studies suggest antimycin A, a common alternative piscicide, typically applied directly to water, may be suitable as an ingested bait. The oral toxicity of antimycin A is not well described. We evaluated the oral toxicity of antimycin A in two carriers (ethanol and corn oil) on grass carp and black carp Mylopharyngodon piceus, administered via gavage. Doses ranged from 1–16 mg/kg. Lethal dose estimates for 50% of treated fish (LD50) were calculated, and the observed treatment levels resulting in complete mortality are reported at 24- and 96-hours post-treatment. Ethanol was a more effective carrier than corn oil with lower LD50 estimates and observed treatment levels with complete mortality. Antimycin A in corn oil produced only partial mortality of black carp even 96 hours from treatment and at the highest dose administered. Results document ingested doses required for mortality of grass carp and black carp that may be used for future development of species-selective antimycin A baits.

Management of Biological Invasions↗

USGS2010

Characterization of water quality and biological communities, Fish Creek, Teton County, Wyoming, 2007-08

Fish Creek, a tributary to the Snake River, is about 25 river kilometers long and is located in Teton County in western Wyoming near the town of Wilson. Public concern about nuisance growths of aquatic plants in Fish Creek have been increasing in recent years. To address this concern, the U.S. Geological Survey conducted a study in cooperation with the Teton Conservation District to characterize the water quality and biological communities in Fish Creek. Water-quality samples were collected for analyses of physical properties and water chemistry (nutrients, nitrate isotopes, and wastewater chemicals) between March 2007 and October 2008 from seven surface-water sites and three groundwater wells. During this same period, aquatic plant and macroinvertebrate samples were collected and habitat characteristics were measured at the surface-water sites. The main objectives of this study were to (1) evaluate nutrient concentrations (that influence biological indicators of eutrophication) and potential sources of nutrients by using stable isotope analysis and other indicator chemicals (such as caffeine and disinfectants) that could provide evidence of anthropogenic sources, such as wastewater or septic tank contamination in Fish Creek and adjacent groundwater, and (2) characterize the algal, macrophyte, and macroinvertebrate communities and habitat of Fish Creek. Nitrate was the dominant species of dissolved nitrogen present in all samples and was the only bioavailable species detected at concentrations greater than the laboratory reporting level in all surface-water samples. Average concentrations of dissolved nitrate in surface water were largest in samples collected from the two sites with seasonal flow near Teton Village and decreased downstream; the smallest concentration was at downstream site A-Wck. Concentrations of dissolved nitrate in groundwater were consistently greater than concentrations in corresponding surface-water sites during the same sampling event. Orthophosphate was the primary dissolved species of phosphorus present in all surface-water and groundwater samples. The average concentration of dissolved orthophosphate in surface water was largest in samples collected from near Teton Village; samples from all other sites had similar average concentrations. Concentrations of dissolved orthophosphate in groundwater also were typically greater than concentrations in corresponding surface-water sites during the same sampling event. The aquatic plant communities in Fish Creek typically were composed of a mixture of macrophytes, macroalgae, microalgae, and moss. The composition of the aquatic plant community in Fish Creek appeared to shift in the downstream direction in 2007. On average, the proportion of macrophytes ranged from about 1 percent at site A-R1U, the most upstream site, to 54 percent of the plant community at site A-R6D, the farthest downstream site sampled during 2007. The downstream increase in macrophytes was accompanied by a downstream decrease in microalgae. The average proportion of microalgae ranged from 80 percent at site A-R1U to 24 percent at site A-R6D. The proportion of the macroalgae Cladophora in the aquatic plant community was relatively high at sites A-Wck and A-R3D in both 2007 and 2008.

Scientific Investigations Report↗

USGS2007

A Quantitative Threats Analysis for the Florida Manatee ( Trichechus manatus latirostris )

The Florida manatee (Trichechus manatus latirostris) is an endangered marine mammal endemic to the southeastern United States. The primary threats to manatee populations are collisions with watercraft and the potential loss of warm-water refuges. For the purposes of listing, recovery, and regulation under the Endangered Species Act (ESA), an understanding of the relative effects of the principal threats is needed. This work is a quantitative approach to threats analysis, grounded in the assumption that an appropriate measure of status under the ESA is based on the risk of extinction, as quantified by the probability of quasi-extinction. This is related to the qualitative threats analyses that are more common under the ESA, but provides an additional level of rigor, objectivity, and integration. In this approach, our philosophy is that analysis of the five threat factors described in Section 4(a)(1) of the ESA can be undertaken within an integrated quantitative framework. The basis of this threats analysis is a comparative population viability analysis. This involves forecasting the Florida manatee population under different scenarios regarding the presence of threats, while accounting for process variation (environmental, demographic, and catastrophic stochasticity) as well as parametric and structural uncertainty. We used the manatee core biological model (CBM) for this viability analysis, and considered the role of five threats: watercraft-related mortality, loss of warm-water habitat in winter, mortality in water-control structures, entanglement, and red tide. All scenarios were run with an underlying parallel structure that allowed a more powerful estimation of the effects of the various threats. The results reflect our understanding of manatee ecology (as captured in the structure of the CBM), our estimates of manatee demography (as described by the parameters in the model), and our characterization of the mechanisms by which the threats act on manatees. As an example of the type of results generated, we estimated that the probability of the manatee population falling to less than 250 adults on either the Atlantic or Gulf coasts (from a current statewide population size of near 3300) within 100 years is 8.6%. Complete removal of the watercraft threat alone would reduce this risk to 0.4%; complete removal of the warm-water threat to 4.2%; removal of both threats would reduce the risk to 0.1%. The modeling approach we have taken also allows us to consider partial removal of threats, as well as removal of multiple threats simultaneously. We believe the measure we have proposed (probability of quasi-extinction over y years, with quasi-extinction defined as dropping below a threshold of z on either coast) is a suitable measure of status that integrates a number of the elements that are relevant to interpretation under the ESA (it directly integrates risk of extinction and reduction of range, and indirectly integrates loss of genetic diversity). But the identification of the time frame of interest and the tolerable risk of quasi-extinction are policy decisions, and an ecology-based quasi-extinction threshold has not yet been determined. We have endeavored to provide results over a wide range of these parameters to give decision-makers useful information to assess status. This assessment of threats suggests that watercraft-related mortality is having the greatest impact on manatee population growth and resilience. Elimination of this single threat would greatly reduce the probability of quasi-extinction. Loss of warm-water is also a significant threat, particularly over the long-term. Red tide and entanglement, while noticeable threats, have had less of an impact on the manatee population. The effect of water control structures may have already been largely mitigated. We did not, however, consider an exhaustive list of threats. Other threats (e.g., reduction of food resources due to storms and development) may play a

Open-File Report↗

USGS2022

Using microbial source tracking to identify fecal contamination sources in Patchogue and Bellport Bays on Long Island, New York

The U.S. Geological Survey worked in cooperation with the New York State Department of Environmental Conservation to assess the potential sources of fecal contamination entering Patchogue and Bellport Bays, two embayments on the south shore of Suffolk County, Long Island, New York. Water samples are routinely collected by the New York State Department of Environmental Conservation in the bays and analyzed for fecal coliform bacteria, an indicator of fecal contamination, to determine the need for closure of shellfish beds for harvest and consumption. Fecal coliform and other bacteria are an indicator of the potential presence of pathogenic (disease-causing) bacteria. However, indicator bacteria alone cannot determine the biological or geographical sources of contamination; therefore, microbial source tracking was implemented to determine various biological sources of contamination. In addition, information such as the location, weather and season, and surrounding land use where a sample was collected help determine the geographical source and conveyance of land-based water to the embayment. Analysis revealed that the most substantial source of fecal contamination to Patchogue and Bellport Bays was discharge from sites draining ponds and wetlands into the rivers and tributaries sampled, particularly during the summer months. Fecal coliform bacteria at sites where ponds and wetlands drain are increased by stormwater runoff, which is another substantial source of fecal contamination. Overall, canine- and waterfowl-associated bacterial contributions were prevalent in source samples in both bays. Human-associated markers were present in surface-water source samples and completely absent in receptor samples in Patchogue Bay. The Fireplace Neck receptor site in Bellport Bay had a human-associated marker present in the summer wet sample only. Human markers were detected at the sample site downstream from the Patchogue wastewater treatment plant but were associated with low fecal coliform concentrations, indicating that the wastewater treatment plant is not a likely source of fecal contamination to Patchogue Bay. The lack of human-associated marker detections within Patchogue and Bellport Bays in summer source samples coupled with low to no detections of fecal coliform, especially where small marinas are present in creeks and tributaries, suggest that boats do not substantially contribute fecal coliform bacteria to the bays. There was little evidence of groundwater-contributing fecal bacteria by direct discharge from the subsurface. Further, the sandy sediment alongside Patchogue and Bellport Bays is unlikely to contribute fecal coliform bacteria from the test host organisms when resuspended in the water column. A classification scheme was developed to convey the degree of fecal contamination to stakeholders and resource managers. Based on this classification scheme, the Corey Creek Near Middle Road, Patchogue River Near Division Street, and Swan River Mouth sampling sites were identified as locations that contribute substantial fecal contamination to Patchogue Bay. In Bellport Bay, the Culvert at Beaverdam Creek site was identified as the location contributing the most substantial fecal contamination.

New York↗

USGS2007

Seabirds as indicators of marine food supplies: Cairns revisited

In his seminal paper about using seabirds as indicators of marine food supplies, Cairns (1987, Biol Oceanogr 5:261–271) predicted that (1) parameters of seabird biology and behavior would vary in curvilinear fashion with changes in food supply, (2) the threshold of prey density over which birds responded would be different for each parameter, and (3) different seabird species would respond differently to variation in food availability depending on foraging behavior and ability to adjust time budgets. We tested these predictions using data collected at colonies of common murre Uria aalge and black-legged kittiwake Rissa tridactyla in Cook Inlet, Alaska. (1) Of 22 seabird responses fitted with linear and non-linear functions, 16 responses exhibited significant curvilinear shapes, and Akaike’s information criterion (AIC) analysis indicated that curvilinear functions provided the best-fitting model for 12 of those. (2) However, there were few differences among parameters in their threshold to prey density, presumably because most responses ultimately depend upon a single threshold for prey acquisition at sea. (3) There were similarities and some differences in how species responded to variability in prey density. Both murres and kittiwakes minimized variability (CV < 15%) in their own body condition and growth of chicks in the face of high annual variability (CV = 69%) in local prey density. Whereas kittiwake breeding success (CV = 63%, r 2 = 0.89) reflected prey variability, murre breeding success did not (CV = 29%, r 2 < 0.00). It appears that murres were able to buffer breeding success by reallocating discretionary ‘loafing’ time to foraging effort in response (r 2 = 0.64) to declining prey density. Kittiwakes had little or no discretionary time, so fledging success was a more direct function of local prey density. Implications of these results for using ‘seabirds as indicators’ are discussed.

Marine Ecology Progress Series↗

USGS1992

Physical oceanographic investigation of Massachusetts and Cape Cod Bays

This physical oceanographic study of the Massachusetts Bays (fig. 1) was designed to provide for the first time a bay-wide description of the circulation and mixing processes on a seasonal basis. Most of the measurements were conducted between April 1990 and June 1991 and consisted of moored observations to study the current flow patterns (fig. 2), hydrographic surveys to document the changes in water properties (fig. 3), high-resolution surveys of velocity and water properties to provide information on the spatial variability of the flow, drifter deployments to measure the currents, and acquisition of satellite images to provide a bay-wide picture of the surface temperature and its spatial variability. A longterm objective of the Massachusetts Bays program is to develop an understanding of the transport of water, dissolved substances and particles throughout the bays. Because horizontal and vertical transport is important to biological, chemical, and geological processes in Massachusetts and Cape Cod Bays, this physical oceanographic study will have broad application and will improve the ability to manage and monitor the water and sediment quality of the Bays. Key results are: There is a marked seasonal variation in stratification in the bays, from well mixed conditions during the winter to strong stratification in the summertime. The stratification acts as a partial barrier to exchange between the surface waters and the deeper waters and causes the motion of the surface waters to be decoupled from the more sluggish flow of the deep waters. During much of the year, there is weak but persistent counterclockwise flow around the bays, made up of southwesterly flow past Cape Ann, southward flow along the western shore, and outflow north of Race Point. The data suggest that this residual flow pattern reverses in fall. Fluctuations caused by wind and density variations are typically larger than the long-term mean. With the exception of western Massachusetts Bay, flushing of the Bays is largely the result of the mean throughflow. Residence time estimates of the surface waters range from 20-45 days. The deeper water has a longer residence time, but its value is difficult to estimate. There is evidence that the deep waters in Stellwagen Basin are not renewed between the onset of stratification and the fall cooling period. Current measurements made near the new outfall site in western Massachusetts Bay suggest that water and material discharged there are not swept away in a consistent direction by a well-defined steady current but are mixed and transported by a variety of processes, including the action of tides, winds, and river inflow. One-day particle excursions are typically less than 10 km. The outfall is apparently located in a region to the west of the basin-wide residual flow pattern. Observations in western Massachusetts Bay, near the location of the future Boston sewage outfall, show that the surficial sediments are episodically resuspended from the seafloor during storms. The observations suggest onshore transport of suspended material during tranquil periods and episodic offshore and southerly alongshore transport of resuspended sediments during storms. The spatial complexity of the flow in the Massachusetts Bays is typical of nearshore areas that have irregular coastal shorelines and topography and currents that are forced locally by wind and river runoff as well as by the flow in adjacent regions. Numerical models are providing a mechanism to interpret the complex spatial flow patterns that cannot be completely resolved by field observations and to investigate key physical processes that control the physics of water and particle transport.

Massachussetts↗

USGS1972

Physical, chemical, and biological aspects of the Duwamish River Estuary, King County, Washington, 1963-67

This report describes the significant results to 1967 of a comprehensive study that began in 1963 to evaluate what changes take place in an estuary as the loads .of raw and partially treated industrial and municipal wastes are replaced by effluent from a secondary treatment plant. The study area is the Duwamish River estuary, about 18.3 river kilometers long. At mean sea level the estuary has a water-surface area of about 1 square mile and a mean width of 440 feet. At the lowest and highest recorded tides, the volume of the estuary is about 205 and 592 million cubic feet, respectively. The estuary is well stratified (salt-wedge type) at fresh-water inflows greater than 1,000 cfs (cubic feet per second), but when inflow rates are less than 1,000 cfs the lower 5.6 kilometers of the estuary grades into the partly mixed type. The crosschannel salinity distribution is uniform for a given location and depth. Salinity migration is controlled by tides and fresh-water inflow. At fresh-water inflow rates greater than 1,000 cfs, water in the upper 8.4 kilometers of the estuary is always fresh regardless of tide. At inflow rates less than 600 cfs and tide heights greater than 10 feet; some salinity has been detected 16.1 kilometers above the mouth of the estuary. Studies using a fluorescent dye show that virtually no downward mixing into the salt wedge occurs; soluble pollutants introduced at the upper end of the estuary stay in the surface layer (5-15 ft thick). On the basis of dye studies when fresh-water inflow is less than 400 cfs, it is estimated that less than 10 percent of a pollutant will remain in the estuary a minimum of 7 days. Longitudinal dispersion coefficients for the surface layer have been determined to be on the order of 100-400 square feet per second. Four water-quality stations automatically monitor DO (dissolved oxygen), water temperature, pH, and specific conductance; at one station solar radiation also is measured. DO concentration in the surface layer decreases almost linearly in a downstream direction. Minimum DO concentration in the surface layer is usually greater than 4 rag/1 (milligrams per liter). The smallest DO values are consistently recorded in the bottom layer at the station 7.7 kilometers above the mouth; monthly means of less than 3 mg/1 of DO have occurred at this point. Manual sampling shows that the DO sag in the bottom layer oscillates between 7.7 and 10.4 kilometers above the mouth of the estuary. Multiple-regression analysis shows that the surface DO content can be estimated from the fresh-water inflow and water temperature. Tidal exchange and fresh-water inflow indirectly control the bottom DO content. Information available from previous studies failed to indicate a progressive decrease in DO content during the period 1949-56, but data from the present study suggest a slight general decrease in the annual minimum DO concentrations in both the upper and lower layers. Average nitrate concentration in fresh water at station 16.2 has increased progressively since 1964, by amounts greater than those which can be attributed to the Renton Treatment Plant, 4.3 kilometers upstream from station 16.2. The BOD (biochemical oxygen demand) in both surface and bottom layers is generally less than 4 rag/1 of oxygen, but values greater than 6 rag/1 have been measured during a period of phytoplankton bloom. Phytoplankton blooms can occur during periods of minimum tidal exchange and fresh-water inflows of less than 300 cfs if solar radiation and water temperature are optimum. Nutrients (nitrogen and phosphorus compounds) do not control the occurrence of a bloom, because sufficient quantities of these nutrients are always present. Nutrients in the treated effluent may increase the biomass of the bloom. Trace-element studies have not defined any role that these elements may play in algal growth. The inflowing fresh water contains principally calcium and bicarbonate and has a dissolved-solids content ra

Water Supply Paper↗