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USGS2017

Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models

“Species distribution modeling” was recently ranked as one of the top five “research fronts” in ecology and the environmental sciences by ISI's Essential Science Indicators (Renner and Warton 2013), reflecting the importance of predicting how species distributions will respond to anthropogenic change. Unfortunately, species distribution models (SDMs) often perform poorly when applied to novel environments. Compounding on this problem is the shortage of methods for evaluating SDMs (hence, we may be getting our predictions wrong and not even know it). Traditional methods for validating SDMs quantify a model's ability to classify locations as used or unused. Instead, we propose to focus on how well SDMs can predict the characteristics of used locations. This subtle shift in viewpoint leads to a more natural and informative evaluation and validation of models across the entire spectrum of SDMs. Through a series of examples, we show how simple graphical methods can help with three fundamental challenges of habitat modeling: identifying missing covariates, non-linearity, and multicollinearity. Identifying habitat characteristics that are not well-predicted by the model can provide insights into variables affecting the distribution of species, suggest appropriate model modifications, and ultimately improve the reliability and generality of conservation and management recommendations.

Ecography↗

USGS2017

Spring fasting behavior in a marine apex predator provides an index of ecosystem productivity

The effects of declining Arctic sea ice on local ecosystem productivity are not well understood but have been shown to vary inter-specifically, spatially, and temporally. Because marine mammals occupy upper trophic levels in Arctic food webs, they may be useful indicators for understanding variation in ecosystem productivity. Polar bears ( Ursus maritimus ) are apex predators that primarily consume benthic and pelagic-feeding ice-associated seals. As such, their productivity integrates sea ice conditions and the ecosystem supporting them. Declining sea ice availability has been linked to negative population effects for polar bears but does not fully explain observed population changes. We examined relationships between spring foraging success of polar bears and sea ice conditions, prey productivity, and general patterns of ecosystem productivity in the Beaufort and Chukchi Seas (CSs). Fasting status (≥7 days) was estimated using serum urea and creatinine levels of 1,448 samples collected from 1,177 adult and subadult bears across three subpopulations. Fasting increased in the Beaufort Sea between 1983–1999 and 2000–2016 and was related to an index of ringed seal body condition. This change was concurrent with declines in body condition of polar bears and observed changes in the diet, condition and/or reproduction of four other vertebrate consumers within the food chain. In contrast, fasting declined in CS polar bears between periods and was less common than in the two Beaufort Sea subpopulations consistent with studies demonstrating higher primary productivity and maintenance or improved body condition in polar bears, ringed seals, and bearded seals despite recent sea ice loss in this region. Consistency between regional and temporal variation in spring polar bear fasting and food web productivity suggests that polar bears may be a useful indicator species. Furthermore, our results suggest that spatial and temporal ecological variation is important in affecting upper trophic-level productivity in these marine ecosystems.

Global Change Biology↗

USGS2012

A horizon scanning assessment of current and potential future threats to migratory shorebirds

We review the conservation issues facing migratory shorebird populations that breed in temperate regions and use wetlands in the non-breeding season. Shorebirds are excellent model organisms for understanding ecological, behavioural and evolutionary processes and are often used as indicators of wetland health. A global team of experienced shorebird researchers identified 45 issues facing these shorebird populations, and divided them into three categories (natural, current anthropogenic and future issues). The natural issues included megatsunamis, volcanoes and regional climate changes, while current anthropogenic threats encompassed agricultural intensification, conversion of tidal flats and coastal wetlands by human infrastructure developments and eutrophication of coastal systems. Possible future threats to shorebirds include microplastics, new means of recreation and infectious diseases. We suggest that this review process be broadened to other taxa to aid the identification and ranking of current and future conservation actions.

Ibis↗

USGS2022

Dermal denticle shedding rates vary between two captive shark species

Shark dermal scale (denticle) accumulation in the fossil record can provide information about the abundance and composition of past shark communities. Denticles are shed continuously, such that a single shark leaves a scattered composite of many isolated denticles in sediments. However, the rate of denticle shedding as well as how these rates vary among shark species with different life modes and their consistency over time are unknown, limiting the interpretation of denticle assemblages. To better understand the process of denticle shedding and calibrate the relationship between absolute shark abundance in the environment and denticle deposition in sediments, we captured denticles shed by 2 shark species in a large aquarium over 9 mo. We then simulated how these aquarium-derived shedding rates shape the relationship between shark abundance and denticle accumulation. Bonnethead sharks Sphyrna tiburo , a more active, benthopelagic species with small, thin denticles, shed 3.6 times faster on average than zebra sharks Stegostoma fasciatum , a more sedentary, demersal species with large, robust denticles. This pattern persisted when shedding rates were corrected by estimated denticle quantities, shark space use, and methodological factors (2.2- to 3.8-fold difference). Over the study, bonnethead shark shedding rates declined while zebra shark shedding rates increased slightly. Finally, denticle assemblage composition corresponded with the relative abundance of denticles on the body of each species, consistent with natural shedding rather than selective loss. Overall, we show that shark taxa contribute unevenly to the denticle record, indicating that shedding rate measurements can help inform and constrain ecological interpretations of denticle assemblages.

Marine Ecology Progress Series↗

USGS2001

Control of ungulate numbers in a protected area

Successful long-term control of ungulate numbers within a protected area requires continuous review and refinement of management practices. Insights gained may have application to other sites. We evaluated management objectives and actions to control populations of exotic axis deer (Axis axis) and fallow deer (Dama dama) at Point Reyes National Seashore, California. Using records of numbers of each species culled from 1968 to 1996 and demographic data, we modeled each population's potential response to management actions and to the cessation of control in 1996. These simulations indicated that control measures hold numbers of both populations below ecological carrying capacity (K) and that populations of fallow and axis deer may have reached K within 5 to 13 years of ceasing control, respectively. We also simulated each population's response to removal of actual numbers of males killed but no females and actual numbers of females killed but no males from 1968 to 1996. Removing males only resulted in both populations reaching K. Removing females only led to the extirpation of both populations. Cessation of control activities prior to removal of all females resulted in recovery of both populations. A team of personnel expended an average of 1.75 work-hours/deer to remove 1,182 exotic deer of both species from 1984 to 1994. The work effort to kill each deer increased 2-fold from 1984 to 1994. The work effort required to remove s2 deer/day reached as great as 20 hours/deer. Elimination of the axis deer population is feasible and likely a more cost-effective management alternative than continued population control. Elimination of fallow deer is potentially more difficult but may be more costeffective than continuing control actions indefinitely. We recommend similar assessments of management alternatives to those charged with controlling ungulate numbers in protected areas.

California↗

USGS2005

Using multiple chemical indicators to assess sources of nitrate and age of groundwater in a karstic spring basin

Human health and ecological concerns have arisen due to a steady increase in nitrate-N concentrations during the past 40 years in Fannin Springs (0.3-4.7 mg/L), a regional discharge point with an average flow of >2.8 m3/second (>100 ft3/second) for water from the karstic Upper Floridan aquifer (UFA). Multiple chemical indicators (major dissolved species, 15N and 18O of nitrate, dissolved gases, 78 pesticides and degradates, and 67 organic compounds typically found in domestic and industrial wastewater) and transient tracers (3H/3He, chlorofluorocarbons [CFCs], sulfur hexafluoride [SF6]) were analyzed in water samples from nine wells along three transects and in spring water to assess groundwater age and potential contaminant sources. Land use is predominantly agricultural (52 percent) and forest (31 percent) in the 320 km2 (124 mi2) spring basin, which was delineated from a potentiometric-surface map of the UFA using high-resolution water-level data. Nitrate-N concentrations were highly variable in the oxic UFA and ranged from <0.02 to 4.7 mg/L. ?? 15N-NO3 values (3.4-9.9 per mil) indicated that nitrate contamination originated from inorganic sources (synthetic fertilizer) and organic sources (manure spreading or waste disposal). Higher nitrate concentrations and the younger age of spring water relative to water from upgradient wells indicate better communication with N sources at the surface. Apparent ages of groundwater correlated positively with well depth (P < 0.05) and were younger in water from wells nearer to the spring (<8 years) compared with other wells (10-50 years). Most transient tracer concentrations were consistent with binary mixing curves representing mixtures of water recharged during the past 10 years and older water (recharged before 1940). Young water mixing fractions ranged from 0.07 to 0.90. Trace levels of herbicides found in groundwater and spring water were indicative of applications for vegetative control in agricultural and other land-use types.

Environmental & Engineering Geoscience↗

USGS2016

Climate change implications for tropical islands: Interpolating and interpreting statistically downscaled GCM projections for management and planning

The potential ecological and economic effects of climate change for tropical islands were studied using output from 12 statistically downscaled general circulation models (GCMs) taking Puerto Rico as a test case. Two model selection/model averaging strategies were used: the average of all available GCMs and the average of the models that are able to reproduce the observed large-scale dynamics that control precipitation over the Caribbean. Five island-wide and multidecadal averages of daily precipitation and temperature were estimated by way of a climatology-informed interpolation of the site-specific downscaled climate model output. Annual cooling degree-days (CDD) were calculated as a proxy index for air-conditioning energy demand, and two measures of annual no-rainfall days were used as drought indices. Holdridge life zone classification was used to map the possible ecological effects of climate change. Precipitation is predicted to decline in both model ensembles, but the decrease was more severe in the “regionally consistent” models. The precipitation declines cause gradual and linear increases in drought intensity and extremes. The warming from the 1960–90 period to the 2071–99 period was 4.6°–9°C depending on the global emission scenarios and location. This warming may cause increases in CDD, and consequently increasing energy demands. Life zones may shift from wetter to drier zones with the possibility of losing most, if not all, of the subtropical rain forests and extinction risks to rain forest specialists or obligates.

Puerto Rico↗

USGS2017

Associations between cyanobacteria and indices of secondary production in the western basin of Lake Erie

Large lakes provide a variety of ecological services to surrounding cities and communities. Many of these services are supported by ecological processes that are threatened by the increasing prevalence of cyanobacterial blooms which occur as aquatic ecosystems experience cultural eutrophication. Over the past 10 yr, Lake Erie experienced cyanobacterial blooms of increasing severity and frequency, which have resulted in impaired drinking water for the surrounding communities. Cyanobacterial blooms may impact ecological processes that support other services, but many of these impacts have not been documented. Secondary production (production of primary consumers) is an important process that supports economically important higher trophic levels. Cyanobacterial blooms may influence secondary production because cyanobacteria are a poor‐quality food resource and cyanotoxins may be harmful to consumers. Over 3 yr at 34 sites across the western basin of Lake Erie, we measured three indices of secondary production that focus on the dominant bivalve taxa: (1) growth of a native unionid mussel, (2) the size of young‐of‐year dreissenid mussels, and (3) the mass of colonizing animals on a Hester‐Dendy sampler. Associations between these indices and cyanobacterial data were estimated to assess whether cyanobacteria are associated with variation in secondary production in the western basin of Lake Erie. The results suggest cyanobacterial abundance alone is only weakly associated with secondary production, but that cyanotoxins have a larger effect on secondary production. Given recurring late‐summer cyanobacterial blooms, this impact on secondary production has the potential to undermine Lake Erie's ability to sustain important ecosystem services.

Lake Erie↗

USGS2025

Characterizing the niche of Phalaris arundinacea (reed canarygrass) in floodplain forests of the Upper Mississippi River

Information on the favorable conditions for invasive species as well as potential constraints to their distribution can be valuable for management efforts. We used a niche modeling approach to analyze the patterns of species distributions along gradients of hypothesized influential environmental variables. Many ecological datasets may have incomplete coverage across the environmental gradients, infrequent sampling under some conditions, insufficient time for an invasive species to occupy all sites, and complex interactions among environmental variables (measured or unmeasured) that may result in species response curves that are difficult to interpret and may be ecologically misleading. To ensure the model and species response curves aligned with ecological niche theory, shape constraints were imposed to guarantee relationships follow a unimodal distribution to reflect the fundamental niche (where a species could occur). We compared a shape-constrained model to an unconstrained model and interpreted the species response curves from the constrained model to better characterize the ecological niche of reed canarygrass in floodplain forests of the Upper Mississippi River, USA. We found the probability of reed canarygrass occurrence decreases with increasing tree canopy cover, tree species richness, distance from forest edge, distance from invaded wet meadows, and island isolation. Probability of reed canarygrass presence exhibited bell-shaped curves in response to hydrology (inundation depth, frequency, and duration) and forest stress metrics indicating an optimum with less favorable conditions on either end of the ecological gradients. This information could be used to prioritize restoration efforts and enhance landcover change research in forested floodplains.

upper Mississippi River↗

USGS2009

Ecological impacts of lead mining on Ozark streams: Toxicity of sediment and pore water

We studied the toxicity of sediments downstream of lead-zinc mining areas in southeast Missouri, using chronic sediment toxicity tests with the amphipod, Hyalella azteca, and pore-water toxicity tests with the daphnid, Ceriodaphnia dubia. Tests conducted in 2002 documented reduced survival of amphipods in stream sediments collected near mining areas and reduced survival and reproduction of daphnids in most pore waters tested. Additional amphipod tests conducted in 2004 documented significant toxic effects of sediments from three streams downstream of mining areas: Strother Creek, West Fork Black River, and Bee Fork. Greatest toxicity occurred in sediments from a 6-km reach of upper Strother Creek, but significant toxic effects occurred in sediments collected at least 14 km downstream of mining in all three watersheds. Toxic effects were significantly correlated with metal concentrations (nickel, zinc, cadmium, and lead) in sediments and pore waters and were generally consistent with predictions of metal toxicity risks based on sediment quality guidelines, although ammonia and manganese may also have contributed to toxicity at a few sites. Responses of amphipods in sediment toxicity tests were significantly correlated with characteristics of benthic invertebrate communities in study streams. These results indicate that toxicity of metals associated with sediments contributes to adverse ecological effects in streams draining the Viburnum Trend mining district.

Ecotoxicology and Environmental Safety↗

USGS2020

Perceived ecological threats and economic benefits of non-native black bass in the United States

Black bass Micropterus spp. are highly sought-after sport fish and, where introduced, are emblematic of the tradeoffs between ensuring productive fisheries and conserving native biodiversity. To disentangle these potentially conflicting interests, we administered a survey of fisheries biologists in the United States to assess perceptions regarding ecological and economic impacts of non-native black bass between anthropogenic and natural habitats. Our results indicate that non-native black bass are generally considered economically beneficial in both habitat types. Contrastingly, these species were perceived to have significantly more negative ecological impacts in natural than anthropogenic habitats. Our findings suggest that habitat may be an important factor to partition the conflicting ecological–economic dynamic of non-native black bass. Implications of this study suggest that challenges remain for managers attempting to balance the paradoxical nature of these species as both desired sport fishes and as potentially harmful invaders when found outside their native range.

Fisheries Magazine↗

USGS2026

Ecological transformations of coastal wetlands of the conterminous United States in response to contemporaneous sea-level rise

Coastal wetlands are among the most important ecosystems on the planet but are increasingly imperiled by accelerating sea-level rise (SLR). In the past, biogeomorphic feedbacks have allowed coastal wetlands to adjust vertically and persist through periods of accelerated SLR. Recent rates of SLR are faster than any in recent geologic history, making the fate of coastal wetlands highly uncertain. Here, we synthesize surface elevation table marker-horizon data from 442 stations in coastal wetlands across the conterminous United States to evaluate if they are largely persisting in the face of accelerated SLR, or if they are undergoing ecological transformations of submergence and/or migration. Across the conterminous United States, 11% of coastal wetlands in this sample are on a trajectory of submergence whereas 73% of sites are lagging SLR, but may be able to migrate upslope, and 16% of sites are gaining elevation at rates which exceed SLR indicating persistence and an ability to migrate seaward. Vulnerability of these systems to ecological transformation varies across the three coasts of the conterminous United States which, span large biogeomorphic gradients. These results serve as one of the first national syntheses of coastal wetland elevation trends and may help focus conservation and restoration efforts in a rapidly changing future.

conterminous United States↗

USGS2012

Bioclimatic predictors for supporting ecological applications in the conterminous United States

The U.S. Geological Survey (USGS) has developed climate indices, referred to as bioclimatic predictors, which highlight climate conditions best related to species physiology. A set of 20 bioclimatic predictors were developed as Geographic Information Systems (GIS) continuous raster surfaces for each year between 1895 and 2009. The Parameter-elevation Regression on Independent Slopes Model (PRISM) and down-scaled PRISM data, which included both averaged multi-year and averaged monthly climate summaries, was used to develop these multi-scale bioclimatic predictors. Bioclimatic predictors capture information about annual conditions (annual mean temperature, annual precipitation, annual range in temperature and precipitation), as well as seasonal mean climate conditions and intra-year seasonality (temperature of the coldest and warmest months, precipitation of the wettest and driest quarters). Examining climate over time is useful when quantifying the effects of climate changes on species' distributions for past, current, and forecasted scenarios. These data, which have not been readily available to scientists, can provide biologists and ecologists with relevant and multi-scaled climate data to augment research on the responses of species to changing climate conditions. The relationships established between species demographics and distributions with bioclimatic predictors can inform land managers of climatic effects on species during decisionmaking processes.

Data Series↗

USGS1992

Riparian vegetation recovery patterns following stream channelization: A geomorphic perspective

Hundreds of kilometres of West Tennessee streams have been channelized since the turn of the century. After a stream is straightened, dredged, or cleared, basinwide ecologic, hydrologic, and geomorphic processes bring about an integrated, characteristic recovery sequence. The rapid pace of channel responses to channelization provides an opportunity to document and interpret vegetation recovery patterns relative to otherwise long—term, concomitant evolution of river geomorphology. Nearly 150 sites along 15 streams were studied in the Obion, Forked Deer, Hatchie, and Wolf River basins. Channels of these streams, except that of the Hatchie River main stem, have undergone major modifications along all or parts of their courses. This paper presents the eco—geomorphic analyses and interpretation of a large multidisciplinary study, with special reference to their interrelated hydrogeomorphic aspects of channel recovery. Quantitative plant ecological analyses were conducted to infer relative bank stability, to identify indicator recovery species, and to determine patterns of vegetation development through the course of accelerated channel evolution. Binary—discriminant and ordination analyses show that distinctive riparian—species patterns reflect a six—stage model of channel evolution and can be used to infer channel stability and hydrogeomorphic conditions. Woody vegetation initially establishes on low— and mid—bank surfaces at the same location and time that bank accretion begins, and corresponds to the site of initial geomorphic restabilization. The linkage of channel bed aggradation, woody vegetation establishment, and bank accretion all lead to recovery of the channel. Pioneer species are hardy and fast growing, and can tolerate moderate amounts of slope instability and sediment deposition; these species include river birch (Betula nigra), black willow (Salix nigra), boxelder (Acer negundo), and silver maple (Acer saccharinum). High stem densities and root—mass development appear to enhance bank stability. Tree—ring analyses suggest that on average 65 yr may be required for recovery after channelization.

Ecology↗

USGS2007

A watershed approach to ecosystem monitoring in Denali National Park and preserve, Alaska

The National Park Service and the National Biological Service initiated research in Denali National Park and Preserve, a 2.4 million-hectare park in southcentral Alaska, to develop ecological monitoring protocols for national parks in the Arctic/Subarctic biogeographic area. We are focusing pilot studies on design questions, on scaling issues and regionalization, ecosystem structure and function, indicator selection and evaluation, and monitoring technologies. Rock Creek, a headwater stream near Denali headquarters, is the ecological scale for initial testing of a watershed ecosystem approach. Our conceptual model embraces principles of the hydrological cycle, hypotheses of global climate change, and biological interactions of organisms occupying intermediate, but poorly studied, positions in Alaskan food webs. The field approach includes hydrological and depositional considerations and a suite of integrated measures linking key aquatic and terrestrial biota, environmental variables, or defined ecological processes, in order to establish ecological conditions and detect, track, and understand mechanisms of environmental change. Our sampling activities include corresponding measures of physical, chemical, and biological attributes in four Rock Creek habitats believed characteristic of the greater system diversity of Denali. This paper gives examples of data sets, program integration and scaling, and research needs.

Journal of the American Water Resources Associatio↗

USGS2021

Hydrologic and ecological investigations in the School Branch watershed, Hendricks County, Indiana—Water years 2016–2018

School Branch in Hendricks County in central Indiana, is a small stream with a variety of agricultural and suburban land uses that drains into the Eagle Creek Reservoir, a major source of drinking water for Indianapolis, Indiana. The School Branch watershed has become the focus of a collaborative partnership of Federal, State, and local agencies; a university research center; and agricultural producers to understand the effects of land use and management practices on water quality and water quantity in the watershed. The U.S. Geological Survey, in cooperation with the Indiana Department of Environmental Management, contributed to the School Branch partnership with the operation of three streamgages (03353415 School Branch at Maloney Road near Brownsburg, Indiana; 03353420 School Branch at County Road 750 North at Brownsburg, Indiana; and 03353430 School Branch at Noble Drive at Brownsburg, Indiana) and the operation of a continuous water-quality gage (also known as a supergage) at County Road 750 North that measured dissolved oxygen, pH, temperature, specific conductance, turbidity, nitrate, and orthophosphate. Additional efforts included the use of passive samplers to identify wastewater indicators; assessment of fish and macroinvertebrate communities and stream habitat to identify ecological impairment; sampling for nutrients and sediment to estimate loads; and using major ions, stable isotopes and nested groundwater monitoring wells at County Road 750 North to determine hydrologic connectivity between the groundwater and surface water. The objectives of this study were to collect surface and groundwater data to analyze the hydrology and water quality within the watershed. Total nitrogen yields were highest at the upstream site, Maloney Road, and indicated a mixture of nitrogen sources in the watershed. Differences found in total nitrogen loading patterns throughout the watershed may be linked to differences in hydrology and land-use management from site to site. The groundwater and surface water were shown to be highly connected, and except for some low-flow periods, the water was flowing from groundwater to the stream for most of the study period. Fish and macroinvertebrate communities show improvement from upstream to downstream, with increases in diversity, richness, and species sensitive to poor water quality and habitat. These increases were most likely due to improved habitat quality at the downstream station.

Indiana↗

USGS2012

Enterococci in the environment

Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.

Microbiology and Molecular Biology Reviews↗

USGS2018

Spatial distribution and ecological risk assessment of heavy metals in coastal surface sediments in the Hebei Province offshore area, Bohai Sea, China

Seven hundred and nine surface sediment samples, along with deeper sediment samples, were collected from Hebei Province along the coastal section of the Bohai Sea, China, and analyzed for grain size, concentrations of organic carbon (Corg) and heavy metals (Cu, Pb, Zn, Cr, Cd, As, and Hg). Results indicated that the average concentrations in the sediments were 16.1 mg/kg (Cu), 19.4 mg/kg (Pb), 50 mg/kg (Zn), 48.8 mg/kg (Cr), 0.1 mg/kg (Cd), 8.4 mg/kg (As), and 20.3 μg/kg (Hg). These concentrations generally met the China Marine Sediment Quality criteria. However, both pollution assessments indicated moderate to strong Cd and Hg contamination in the study area. The potential ecological risk index suggested that the combined ecological risk of the seven studied metals may be low, but that 24.5% of the sites, where sediments were more finer and higher in Corg concentration, had high ecological risk in Hg and Cd pollution.

Bohai Sea, Hebei Province↗