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USGS2013

Ecological limit functions relating fish community response to hydrologic departures of the ecological flow regime in the Tennessee River basin, United States

Ecological limit functions relating streamflow and aquatic ecosystems remain elusive despite decades of research. We investigated functional relationships between species richness and changes in streamflow characteristics at 662 fish sampling sites in the Tennessee River basin. Our approach included the following: (1) a brief summary of relevant literature on functional relations between fish and streamflow, (2) the development of ecological limit functions that describe the strongest discernible relationships between fish species richness and streamflow characteristics, (3) the evaluation of proposed definitions of hydrologic reference conditions, and (4) an investigation of the internal structures of wedge-shaped distributions underlying ecological limit functions. Twenty-one ecological limit functions were developed across three ecoregions that relate the species richness of 11 fish groups and departures from hydrologic reference conditions using multivariate and quantile regression methods. Each negatively sloped function is described using up to four streamflow characteristics expressed in terms of cumulative departure from hydrologic reference conditions. Negative slopes indicate increased departure results in decreased species richness. Sites with the highest measured fish species richness generally had near-reference hydrologic conditions for a given ecoregion. Hydrology did not generally differ between sites with the highest and lowest fish species richness, indicating that other environmental factors likely limit species richness at sites with reference hydrology. Use of ecological limit functions to make decisions regarding proposed hydrologic regime changes, although commonly presented as a management tool, is not as straightforward or informative as often assumed. We contend that statistical evaluation of the internal wedge structure below limit functions may provide a probabilistic understanding of how aquatic ecology is influenced by altered hydrology and may serve as the basis for evaluating the potential effect of proposed hydrologic changes.

Tennessee River basin↗

USGS2004

Environmental setting, water quality, and ecological indicators of surface-water quality in the Mermentau River Basin, southwestern Louisiana, 1998-2001

The U.S. Geological Survey collected data from 29 wells and 24 surface-water sites in the Mermentau River Basin, 1998-2001, to better understand ground-water and surface-water quality; aquatic invertebrate communities; and habitat conditions, in relation to land use. This study was apart of the National Water-Quality Assessment Program, which was designed to assess water quality as it relates to various land uses. Water-quality data were evaluated with criteria established for the protection of drinking water and aquatic life, and bed-sediment data were compared to aquatic life criteria. Water-quality and ecological data were analyzed statistically in relation to drainage area and agricultural land-use integrity. Concentrations of nutrients and major inorganic ions in ground water and surface water generally were highest in the southeastern part of the study area where soils contain thick loess deposits. Peak concentrations of nutrients in surface water occurred March-may at two sites with high agricultural intensity; the lowest concentrations occurred August-January. The greatest potential for eutrophic conditions in surface water, based on nutrient concentrations, existed March-May, at about the same time or shortly after ricefields were drained. Secondary Maximum Contaminant Levels established by the U.S. Environmental Protection Agency (USEPA) were exceeded for sulfate, chloride, iron, or manganese in samples from 20 wells, and for iron or manganese in samples from all surface-water sites. Fewer pesticides were detected in ground water than in surface water. In 11 of of the 29 wells sampled, at least one pesticide or pesticide degradation product was detected. The most frequently detected pesticides or pesticide degradation products in ground water were the herbicides benzaton and atrazine. Concentrations of 47 pesticides and degradation products were detected in surface water. At least 3 pesticides were detected in all surface-water samples. In 72 percent of the samples at least 5 hydrophilic pesticides were detected, and in more than 70 percent of the samples at least 3 hydrophobic pesticides were detected. Although atrazine concentrations in three samples collected in the spring exceeded 3 micrograms per liter, the USEPA Maximum Contaminant Level of 3 micrograms per liter was not exceeded because it is based on an annual average of quarterly samples. Concentrations larger than 3.0 micrograms per liter were not detected in samples collected during other times of the year. Tebuthiuron was detected at all surface-water sites; the largest concentration (6.33 micrograms per liter) was detected at a site on Bayou des Cannes, and was the only detection that exceeded the criterion (1.6 micrograms per liter) for the protection of aquatic life. Malathion was detected at 16 surface-water sites; the largest concentration (0.113 micrograms per liter) was detected at a site on Bayou Lacassine and was the only detection that exceeded the criterion (0.1 micrograms per liter) for the protection of aquatic life. Concentrations of fipronil exceeded numeric targets for acute total maximum daily loads (2.3 micrograms per liter) at 3 sites and chronic total maximum daily loads (4.6 micrograms per liter) at 14 sites. Maximum pesticide concentrations in surface water usually occurred in the spring at about the same time or shortly after ricefields were drained. Concentrations of DDE in bed sediment at two sites exceeded interim freshwater sediment quality guidelines for the protection of aquatic life. Fipronil sulfide and desulfinylpronil were detected at all 17 sites from which bed-sediment samples were collected, but there are no current (2002) guidelines with which to evaluate the environmental effects of fipronil and degradation products. Two methods were used to group the ecological data-collection sites: (1) Sites were grouped before data collection (according to the study design) using drainage area

Water-Resources Investigations Report↗

USGS2025

Mapping ecological states in the upper Colorado River basin: Implications for fire management

Spatially explicit information on ecosystem dynamics that offers a mechanistic understanding of ecological processes can benefit environmental management. Broad-scale maps based on state-and-transition models provide valuable insight into transitions among ecological states resulting from specific drivers within areas sharing similar climatic and edaphic characteristics ecological sites (ES). We aimed to quantify ecological dynamics of two ES groups in the Upper Colorado River Basin from 1986 to 2022 through annual maps of ecological states and assess potential drivers of observed state change. This region comprises important sagebrush shrublands and pinyon-juniper woodlands affected by non-native annual grass invasion, wildfires, and drought-induced tree mortality. Using field-based and remote sensing data, we modeled vegetation states using random forest models and mapped the states annually from 1986 to 2022. To demonstrate the utility of the state maps for monitoring and management, we used this time series of maps to investigate the influences of fire and drought on state occurrence. Our findings revealed a statistically significant increase in states invaded by non-native annual species (Invaded state), which replaced Grassland and Shrubland states, while Shrubland states decreased significantly, transitioning to invaded and Woodland states. Invaded states had the highest likelihood of burning, followed by Woodlands. Drought was associated with increased area of Grassland and Bare states, but with decreased area of invaded and Shrubland states. These results indicate an accelerating fire cycle is potentially leading to ongoing regional environmental degradation. Despite increasing drought conditions during the study period, the invaded states continued to increase in area, indicating additional underlying mechanisms. Our reproducible, broad-scale, ecologically-driven state mapping process enhances understanding of how drought, fire, and invasion by non-native plants can transform semiarid landscapes of the western USA.

Arizona, Colorado, New Mexico, Utah, Wyoming↗

USGS2018

Use of remote sensing to detect and predict aquatic nuisance vegetation growth in coastal Louisiana: Summary of findings

On an annual basis, federal and state agencies are responsible for mapping and removing large expanses of aquatic nuisance vegetation from navigable waterways. This study set out to achieve four primary objectives: (1) utilize recent advancements in remote sensing techniques to classify the extent and distribution of aquatic vegetation in coastal ecosystems using satellite imagery, (2) assess primary aquatic vegetation growth and management efforts in coastal Louisiana, (3) statistically identify the ecological drivers that promote growth and infestation of aquatic nuisance vegetation, and (4) develop numerical models and a spatial tool to predict the probability of occurrence and growth of aquatic vegetation given ecological drivers. Moderate spatial resolution multispectral satellite imagery were used in conjunction with environmental variables from available data streams to generate regression models that predict aquatic vegetation occurrence in the eastern coastal region of south Louisiana. Geospatial tools were developed to execute the model logic using recent environmental conditions, thereby predicting aquatic vegetation occurrence and producing classified maps for end users. These products provide more efficient and enhanced capabilities for management of aquatic nuisance vegetation.

Louisiana↗

USGS2021

Occurrence, fate, and transport of aerially applied herbicides to control invasive buffelgrass within Saguaro National Park Rincon Mountain District, Arizona, 2015–18

The spread of the invasive and fire-adapted buffelgrass ( Cenchrus ciliaris L.) threatens desert ecosystems by competing for resources, increasing fuel loads, and creating wildfire connectivity. The Rincon Mountain District of Saguaro National Park addressed this natural resource threat with the use of glyphosate-based herbicides (GBHs). In 2010, the Rincon Mountain District initiated an aerial restoration plan to control dense buffelgrass patches in remote areas and implemented a trial project to evaluate the effects of aerial restoration techniques that included the helicopter application of GBHs. In 2014, more than 250 acres of buffelgrass in the Rincon Mountain District were treated with the aerial application of GBHs. This widespread aerial application of GBHs continued through 2018, but the potential transport and effects to aquatic ecosystems were unknown. In 2015–18, the U.S. Geological Survey, in cooperation with the National Park Service, studied the occurrence, distribution, fate, and transport of glyphosate in surface water and sediments derived from areas that were treated during past and current aerial herbicide applications. Three watersheds, treated with different regimens of GBHs, were sampled for glyphosate and the primary metabolite of glyphosate, aminomethylphosphonic acid (AMPA), during various hydrologic flow conditions. Water and aquatic sediment were collected from three watersheds, each in a different stage of application during the U.S. Geological Survey study. The unnamed watershed above the Loma Verde Trailhead referred to by the National Park Service as “Loma Verde canyon” had received no aerial treatment since 2014, whereas the Box Canyon watershed was aerially treated every year beginning in 2014. The Madrona Canyon watershed was first sprayed in 2016 and aerial application continued once a year though the entirety of the study. In addition, terrestrial soil samples were sampled from areas sprayed to understand dissipation rates and herbicide transport via sediments washing away during rainfall runoff. The concentrations present in water and sediment samples were compared to ecological benchmarks and characterized within the context of the environmental conditions of the park setting. Of the 48 water samples collected and analyzed for glyphosate and AMPA, 10.4 percent and 14.6 percent were detected above the laboratory minimum detection limit, respectively. Mean water concentrations, calculated using specific statistical methods for non-detects, were equal to the laboratory minimum detection limit of 0.02 microgram per liter for samples collected in all the watersheds. In aquatic sediments, glyphosate and AMPA were detected in 10.7 and 25.0 percent of the samples, whereas 89.5 and 100 percent of the terrestrial soil samples had detections for glyphosate and AMPA, respectively. Mean aquatic sediment concentrations were 1.13 and 4.42 micrograms per kilogram (μg/kg) for glyphosate and AMPA, respectively. Mean terrestrial soil concentrations were orders of magnitude greater than water and aquatic sediment with concentrations of 678 μg/kg for AMPA and 1,240 μg/kg for glyphosate. Hours after glyphosate-based herbicide was applied, the concentrations of glyphosate and AMPA were present in terrestrial soil samples near or above the laboratory maximum detection limit of 5,000 μg/kg. The Box Canyon watershed was the most intensively treated watershed in terms of total land area treated, total amount of GBH applied, and number of years treated. The frequent and large volume of treatment resulted in the highest number of detections of glyphosate and AMPA in water (3 and 7 detections, respectively) and in aquatic sediment (2 and 6 detections, respectively) samples. In comparison, the other two watersheds had two or fewer detections for glyphosate and AMPA in water and aquatic sediment. Glyphosate detected in pools was associated with increased rainfall closer in time to the last herbicide treatment. Glyphosate and AMPA concentration ratios above one, along with stable-isotope and tritium results, indicated that runoff processes were the primary transport mechanism for the two compounds when found in streams and pools rather than subsurface recharge or deeper flow paths. One pool in a small tributary of Box Canyon consistently had detections of glyphosate and AMPA in aquatic sediments, but these frequent concentrations were likely related to the intensive application upstream, near the steep terrain above the head of the channel that supplies the downstream pool. Intense flows during summer rainfall events move treated sediments into this channel where vegetation and the incised bedrock banks of the pool retained those sediments and ultimately led to frequent detections of both compounds. Isotope results in most of the pools and tinajas indicated that the water source had residence time representative of recently recharged waters, on the order of years. No water concentrations exceeded published criteria for human health or aquatic life. Median and maximum glyphosate and AMPA water concentrations were lower than those reported in other national assessments, but maximum concentrations observed in individual runoff samples were higher than median concentrations measured in the national assessments. A similar finding was observed with aquatic sediment concentrations measured in the Rincon Mountain District. Results from the study were compared and assessed in the context of other studies examining GBHs and their effects on amphibians, fish, and macroinvertebrates. This comparison was used to generalize the potential risk to aquatic species similar to those species in the Rincon Mountain District. Concentrations of published effect levels were several orders of magnitude greater than the highest concentration detected in water at the Rincon Mountain District. Most published studies evaluate acute and chronic toxicity for glyphosate and GBHs, and these criteria may not be representative of environmental conditions in the Rincon Mountain District. The classic lethal dose studies conducted in a controlled laboratory setting may not be suitable for comparison to the longer, variable, low-dose exposure conditions in the pools and tinajas in the Rincon Mountain District. However, this study determined that the fate of GBHs transported from treated areas to potential aquatic habitat was highly variable in occurrence, timing, and concentrations. This variability in glyphosate concentrations was too high, and the potential exposure was determined to be far too complex to directly compare with the results from controlled studies. This study provides the first information collected on GBHs used to control invasive buffelgrass in a remote, mountainous, and semiarid setting. The information about the transport and fate of herbicide application near aquatic habitat will help to inform managers about the broader ecosystem implications and provide useful information to other agencies implementing buffelgrass remediation strategies near aquatic habitat.

Arizona↗

USGS2019

Using the beta distribution to analyze plant cover data

Most plant species are spatially aggregated. Local demographic and ecological processes (e.g. vegetative growth and limited seed dispersal) result in a clustered spatial pattern within an environmentally homogenous area. Spatial aggregation should be considered when modelling plant abundance data. Commonly, plant abundance is quantified by measuring cover within multiple areal plots or along multiple lines randomly placed within a study area. A common practice for analyzing plant cover is to use statistical methods that rely on the normal distribution for quantifying uncertainty. This is problematic because plant cover data tend to be left‐skewed (J‐shaped), right skewed (L‐shaped) or U‐shaped and, therefore, commonly violate classic statistical assumptions, such as normality. We outline statistical analyses that explicitly account for spatial aggregation by assuming that plant cover is beta‐distributed. The beta distribution is a flexible choice because within the open unit interval it can take on a wide range of shapes (L, J, U, or a bell‐shaped). We discuss and introduce extensions to the beta distribution that address common analysis issues encountered in plant cover datasets, such as i) the treatment of zero and one cover values, ii) hierarchical data structures, and iii) observations errors. For heuristic purposes, we focus on single species analyses, but we demonstrate how the outlined methods can be generalized to more species. The assumption that plant cover is beta‐distributed allows us to estimate the degree of spatial aggregation, and the ecological significance of this new knowledge is discussed. We provide a summary of available software for analyses (emphasizing standard R packages) and include worked examples and a simulation study comparing analysis options as supplemental information. Synthesis . Previously, the state of the statistical software made it practically difficult for empirical plant ecologists to analyze their cover data correctly, but new theory and R‐packages have been developed, and this difficulty no longer exists. We recommend that empirical plant ecologists embrace the new statistical possibilities for exploring the exciting ecological features in spatial variation of plant cover.

Journal of Ecology↗

USGS2012

Estimation of baseline daily mean streamflows for ungaged locations on Pennsylvania streams, water years 1960-2008

Water-resource managers use daily mean streamflows to generate streamflow statistics and analyze streamflow conditions. An in-depth evaluation of flow regimes to promote instream ecological health often requires streamflow information obtainable only from a time series hydrograph. Historically, it has been difficult to estimate daily mean streamflow for an ungaged location. The U.S. Geological Survey (USGS), in cooperation with the Pennsylvania Department of Environmental Protection, Susquehanna River Basin Commission, and The Nature Conservancy, has developed the Ba seline S treamflow E stimator (BaSE) to estimate baseline streamflow at a daily time scale for ungaged streams in Pennsylvania using data collected during water years 1960–2008. Baseline streamflow is minimally altered by regulation, diversion, or mining, and other anthropogenic activities. Daily mean streamflow is estimated in BaSE using a methodology that equates streamflow as a percentile from a flow duration curve for a particular day at an ungaged location with streamflow as a percentile from the flow duration curve for the same day at a reference streamgage that is considered to be hydrologically similar to the ungaged location. An appropriate reference streamgage is selected using map correlation, in which variogram models are developed that correlate streamflow at one streamgage with streamflows at all other streamgages. The percentiles from a flow duration curve for the ungaged location are converted to streamflow through the use of regression equations. Regression equations used to predict 17 flow-duration exceedance probabilities were developed for Pennsylvania using geographic information system-derived basin characteristics. The standard error of prediction for the regression equations ranged from 11 percent to 92 percent with the mean of 31 percent. The map correlation method for estimating streamflow was tested at locations within two pilot basins, the Upper Delaware River Basin and the Lower Susquehanna River Basin, before being applied statewide. Reference streamgages within the pilot basins were used as ungaged locations for analyzing the map correlation method. Correlation using Spearman’s rho and centroid distance performed as well as, or better than, the method using the closest streamgage as a reference streamgage. Map correlation using the correlation metrics identified in the pilot basins was applied to 156 streamgages in and near Pennsylvania. BaSE uses the map correlation method and flow-duration exceedance probability regression equations to estimate baseline daily mean streamflow for an ungaged location. The output from BaSE is a Microsoft Excel® report file that summarizes the reference streamgage and ungaged location information, including basin characteristics, percent difference in basin characteristics between the two locations, any warning associated with the basin characteristics, mean and median streamflow for the ungaged location, and a daily hydrograph of streamflow for water years 1960–2008 for the ungaged location. The daily mean streamflow for the ungaged location can be exported as a text file to be used as input into other statistical software packages. BaSE estimates daily mean streamflow for baseline conditions only, and any alterations to streamflow from regulation, large water use, or substantial mining are not reflected in the estimated streamflow.

Pennsylvania↗

USGS2019

Reduced soil macropores and forest cover reduce warm-season baseflow below ecological thresholds in the upper Delaware River Basin

We examined the impacts of changes in land cover and soil conditions on the flow regime of the upper Delaware River Basin using the Water Availability Tool for Environmental Resources (WATER). We simulated flows for two periods, circa 1600 and 1940, at three sites using the same temperature and precipitation conditions: the East Branch (EB), West Branch (WB), and mainstem Delaware River at Callicoon, NY. The 1600 period represented pristine forest and soils. The 1940 period included reduced forest cover, increased agriculture, and degraded soils with reduced soil macropore fractions. A model-sensitivity test examined the impact of soil macropore and land cover change separately. We assessed changes in flow regimes between the 1600 and 1940 periods using a variety of flow statistics, including established ecological limits of hydrologic alteration (ELOHA) thresholds. Reduced forest soil macropore fraction significantly reduced summer and fall base flows. The 1940 period had significantly lower Q50 flows (50% exceedance) than the 1600 period, as well as summer and fall Q90 and Q75-90 flows below the ELOHA thresholds. The 1- to 7-day minimum flows were also lower for the 1940 period, by 17% on the mainstem. 1940 flows were 6% more likely than the 1600 period to fall below the low-flow threshold for federally endangered dwarf wedgemussel (Alasmidonta heterodon) habitat. In contrast, the 1940 period had higher flows than the 1600 period from late fall to early winter.

New York, Pennsylvania↗

USGS2013

Phylogenetic conservatism in plant phenology

Phenological events – deﬁned points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reﬂecting ﬂexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency for closely related spe-cies to share similar ecological and biological attributes – in phenological traits across ﬂowering plants. We aggregated published and unpublished data on timing of ﬁrst ﬂower and ﬁrst leaf, encompassing ~4000 species at 23 sites across the Northern Hemisphere. We reconstructed the phylogeny for the setof included species, ﬁrst, using the software program Phylomatic, and second, from DNA data. We then quantiﬁed phylogenetic conservatism in plant phenology within and across sites. We show that more closely related species tend to ﬂower and leaf at similar times. By contrastingmean ﬂowering times within and across sites, however, we illustrate that it is not the time of yearthat is conserved, but rather the phenological responses to a common set of abiotic cues. Our ﬁndings suggest that species cannot be treated as statistically independent when modelling phenological responses. Synthesis. Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conser ved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species’ shared evolutionary histories.

Journal of Ecology↗

USGS2017

A three-dimensional mapping of the ocean based on environmental data

The existence, sources, distribution, circulation, and physicochemical nature of macroscale oceanic water bodies have long been a focus of oceanographic inquiry. Building on that work, this paper describes an objectively derived and globally comprehensive set of 37 distinct volumetric region units, called ecological marine units (EMUs). They are constructed on a regularly spaced ocean point-mesh grid, from sea surface to seafloor, and attributed with data from the 2013 World Ocean Atlas version 2. The point attribute data are the means of the decadal averages from a 57-year climatology of six physical and chemical environment parameters (temperature, salinity, dissolved oxygen, nitrate, phosphate, and silicate). The database includes over 52 million points that depict the global ocean in x, y, and z dimensions. The point data were statistically clustered to define the 37 EMUs, which represent physically and chemically distinct water volumes based on spatial variation in the six marine environmental characteristics used. The aspatial clustering to produce the 37 EMUs did not include point location or depth as a determinant, yet strong geographic and vertical separation was observed. Twenty-two of the 37 EMUs are globally or regionally extensive, and account for 99% of the ocean volume, while the remaining 15 are smaller and shallower, and occur around coastal features. We assessed the vertical distribution of EMUs in the water column and placed them into classical depth zones representing epipelagic (0 m to 200 m), mesopelagic (200 m to 1,000 m), bathypelagic (1,000 m to 4,000 m) and abyssopelagic (>4,000 m) layers. The mapping and characterization of the EMUs represent a new spatial framework for organizing and understanding the physical, chemical, and ultimately biological properties and processes of oceanic water bodies. The EMUs are an initial objective partitioning of the ocean using long-term historical average data, and could be extended in the future by adding new classification variables and by introducing functionality to develop time-specific EMU distribution maps. The EMUs are an open-access resource, and as both a standardized geographic framework and a baseline physicochemical characterization of the oceanic environment, they are intended to be useful for disturbance assessments, ecosystem accounting exercises, conservation priority setting, and marine protected area network design, along with other research and management applications.

Oceanography↗

USGS2023

Characterization of fish assemblages in eleven multi-use reservoirs from North Carolina, USA

Managing impounded river systems is a recurring challenge for aquatic resource professionals because reservoirs serve multiple functions with different ecological and socioeconomic outcomes. However, research on fishes in reservoirs has disproportionally focused on recreationally and economically important species, with less attention directed toward fish assemblages despite the potential for management at the assemblage level. As such, evaluation of relationships between reservoir fish assemblages and biotic and abiotic factors and testing whether assemblage structure is affected by changing environmental conditions may deepen ecological understanding and provide insights for reservoir fisheries management. Our overall objective was to assess these relationships in 11 reservoirs from North Carolina, USA. We sampled fish assemblages in the reservoirs, which spanned five river basins representing a range of habitat conditions, using experimental gillnets and pulsed DC nighttime electrofishing. Multivariate statistical analyses indicated that taxonomic differences in fish assemblage composition among river basins followed a gradient of productivity. The top contributing species to reservoir dissimilarity were bluegill ( Lepomis macrochirus ), gizzard shad ( Dorosoma cepedianum ), black crappie ( Pomoxis nigromaculatus ), and white perch ( Morone americana ). These four species were positively associated with factors that reflect increasing eutrophic conditions in the 11 reservoirs and could, therefore, serve as indicators of reservoir productivity, anthropogenic influence, and fish assemblage structure, in addition to their key role in reservoir fisheries management. Whereas fisheries research has historically focused on assessing fish populations, our results illustrate the ecological and management insights derived from simultaneously collecting assemblage- and population-level data. Research on reservoir fish assemblages in relation to biotic and abiotic conditions may help advance fish ecology and management alike.

North Carolina↗

USGS2001

The status of the macroinvertebrate community in the St. Croix River, Minnesota and Wisconsin: An examination of ecological health using techniques of multivariate analysis

A statistical procedure that integrates physical, chemical and biological data is used to operationally define and analyze ecological health. Benthic macroinvertebrates collected from May through September from eight locations along the St. Croix River in Minnesota and Wisconsin were analyzed by canonical correspondence analyses. A sequential multivariate analysis procedure was developed that included: 1) determining which environmental variables explained the most variation in the taxonomic data, individually and collectively, 2) running canonical correspondence analyses on the taxonomic data along with environmental variables chosen from a stepwise forward selection procedure, 3) performing a cluster analysis of the taxonomic data in sampling times to determine artificial biological seasons, and 4) analyzing the seasonal data (three time intervals) separately, as in steps 1 and 2. Changes in community structure were significantly associated with changes in environmental factors (physical and chemical) that varied in time and space. The variables found to be significant were largely those expected to be associated with the variations in the structure of benthic macroinvertebrate community in an unimpacted river. A slight influence of nitrogen could be detected in agricultural areas.

Minnesota, Wisconsin↗

USGS2012

Perils of correlating CUSUM-transformed variables to infer ecological relationships (Breton et al. 2006; Glibert 2010)

We comment on a nonstandard statistical treatment of time-series data first published by Breton et al. (2006) in Limnology and Oceanography and, more recently, used by Glibert (2010) in Reviews in Fisheries Science. In both papers, the authors make strong inferences about the underlying causes of population variability based on correlations between cumulative sum (CUSUM) transformations of organism abundances and environmental variables. Breton et al. (2006) reported correlations between CUSUM-transformed values of diatom biomass in Belgian coastal waters and the North Atlantic Oscillation, and between meteorological and hydrological variables. Each correlation of CUSUM-transformed variables was judged to be statistically significant. On the basis of these correlations, Breton et al. (2006) developed "the first evidence of synergy between climate and human-induced river-based nitrate inputs with respect to their effects on the magnitude of spring Phaeocystis colony blooms and their dominance over diatoms."

Limnology and Oceanography↗

USGS2013

The Hyper-Envelope Modeling Interface (HEMI): A Novel Approach Illustrated Through Predicting Tamarisk ( Tamarix spp.) Habitat in the Western USA

Habitat suitability maps are commonly created by modeling a species’ environmental niche from occurrences and environmental characteristics. Here, we introduce the hyper-envelope modeling interface (HEMI), providing a new method for creating habitat suitability models using Bezier surfaces to model a species niche in environmental space. HEMI allows modeled surfaces to be visualized and edited in environmental space based on expert knowledge and does not require absence points for model development. The modeled surfaces require relatively few parameters compared to similar modeling approaches and may produce models that better match ecological niche theory. As a case study, we modeled the invasive species tamarisk ( Tamarix spp.) in the western USA. We compare results from HEMI with those from existing similar modeling approaches (including BioClim, BioMapper, and Maxent). We used synthetic surfaces to create visualizations of the various models in environmental space and used modified area under the curve (AUC) statistic and akaike information criterion (AIC) as measures of model performance. We show that HEMI produced slightly better AUC values, except for Maxent and better AIC values overall. HEMI created a model with only ten parameters while Maxent produced a model with over 100 and BioClim used only eight. Additionally, HEMI allowed visualization and editing of the model in environmental space to develop alternative potential habitat scenarios. The use of Bezier surfaces can provide simple models that match our expectations of biological niche models and, at least in some cases, out-perform more complex approaches.

Environmental Management↗

USGS2023

BatTool: Projecting bat populations facing multiple stressors using a demographic model

Bats provide ecologically and agriculturally important ecosystem services but are currently experiencing population declines caused by multiple environmental stressors, including mortality from white-nose syndrome and wind energy development. Analyses of the current and future health and viability of these species may support conservation management decision making. Demographic modeling provides a quantitative tool for decision makers and conservation managers to make more informed decisions, but widespread adoption of these tools can be limited because of the complexity of the mathematical, statistical, and computational components involved in implementing these models. In this work, we provide an exposition of the BatTool R package, detailing the primary components of the matrix projection model, a publicly accessible graphical user interface ( https://rconnect.usgs.gov/battool ) facilitating user-defined scenario analyses, and its intended uses and limitations (Wiens et al., US Geol Surv Data Release 2022; Wiens et al., US Geol Surv Softw Release 2022). We present a case study involving wind energy permitting, weighing the effects of potential mortality caused by a hypothetical wind energy facility on the projected abundance of four imperiled bat species in the Midwestern United States.

Methods in Ecology and Evolution↗

USGS2021

Biogeography and ecology of Ostracoda in the U.S. northern Bering, Chukchi, and Beaufort Seas

Ostracoda (bivalved Crustacea) comprise a significant part of the benthic meiofauna in the Pacific-Arctic region, including more than 50 species, many with identifiable ecological tolerances. These species hold potential as useful indicators of past and future ecosystem changes. In this study, we examined benthic ostracodes from nearly 300 surface sediment samples, >34,000 specimens, from three regions—the northern Bering, Chukchi and Beaufort Seas—to establish species’ ecology and distribution. Samples were collected during various sampling programs from 1970 through 2018 on the continental shelves at 20 to ~100m water depth. Ordination analyses using species’ relative frequencies identified six species, Normanicythere leioderma , Sarsicytheridea bradii , Paracyprideis pseudopunctillata , Semicytherura complanata , Schizocythere ikeyai , and Munseyella mananensis , as having diagnostic habitat ranges in bottom water temperatures, salinities, sediment substrates and/or food sources. Species relative abundances and distributions can be used to infer past bottom environmental conditions in sediment archives for paleo-reconstructions and to characterize potential changes in Pacific-Arctic ecosystems in future sampling studies. Statistical analyses further showed ostracode assemblages grouped by the summer water masses influencing the area. Offshore-to-nearshore transects of samples across different water masses showed that complex water mass characteristics, such as bottom temperature, productivity, as well as sediment texture, influenced the relative frequencies of ostracode species over small spatial scales. On the larger biogeographic scale, synoptic ordination analyses showed dominant species— N . leioderma (Bering Sea), P . pseudopunctillata (offshore Chukchi and Beaufort Seas), and S . bradii (all regions)—remained fairly constant over recent decades. However, during 2013–2018, northern Pacific species M . mananensis and S . ikeyai increased in abundance by small but significant proportions in the Chukchi Sea region compared to earlier years. It is yet unclear if these assemblage changes signify a meiofaunal response to changing water mass properties and if this trend will continue in the future. Our new ecological data on ostracode species and biogeography suggest these hypotheses can be tested with future benthic monitoring efforts.

PLoS ONE↗

USGS2012

Application of empirical predictive modeling using conventional and alternative fecal indicator bacteria in eastern North Carolina waters

Coastal and estuarine waters are the site of intense anthropogenic influence with concomitant use for recreation and seafood harvesting. Therefore, coastal and estuarine water quality has a direct impact on human health. In eastern North Carolina (NC) there are over 240 recreational and 1025 shellfish harvesting water quality monitoring sites that are regularly assessed. Because of the large number of sites, sampling frequency is often only on a weekly basis. This frequency, along with an 18–24 h incubation time for fecal indicator bacteria (FIB) enumeration via culture-based methods, reduces the efficiency of the public notification process. In states like NC where beach monitoring resources are limited but historical data are plentiful, predictive models may offer an improvement for monitoring and notification by providing real-time FIB estimates. In this study, water samples were collected during 12 dry (n = 88) and 13 wet (n = 66) weather events at up to 10 sites. Statistical predictive models for Escherichiacoli (EC), enterococci (ENT), and members of the Bacteroidales group were created and subsequently validated. Our results showed that models for EC and ENT (adjusted R2 were 0.61 and 0.64, respectively) incorporated a range of antecedent rainfall, climate, and environmental variables. The most important variables for EC and ENT models were 5-day antecedent rainfall, dissolved oxygen, and salinity. These models successfully predicted FIB levels over a wide range of conditions with a 3% (EC model) and 9% (ENT model) overall error rate for recreational threshold values and a 0% (EC model) overall error rate for shellfish threshold values. Though modeling of members of the Bacteroidales group had less predictive ability (adjusted R 2 were 0.56 and 0.53 for fecal Bacteroides spp. and human Bacteroides spp., respectively), the modeling approach and testing provided information on Bacteroidales ecology. This is the first example of a set of successful statistical predictive models appropriate for assessment of both recreational and shellfish harvesting water quality in estuarine waters.

North Carolina↗

USGS2019

Assessing the hydrologic impact of historical railroad embankments on wetland vegetation response in Canaan Valley, WV (USA): The value of high-resolution data

The recovery of natural ecological processes after disturbance is poorly understood. Some disturbances may be so severe as to set ecosystems onto a new trajectory. The Canaan Valley National Wildlife Refuge in West Virginia protects a unique high-altitude wetland that was heavily disturbed by logging 100 years BP and has since transitioned to a new ecological state (shrub wetland). Refuge managers interested in preserving and restoring ecosystem states expressed concerned about lingering impacts of previous disturbances (logging, railroads, beaver, deer, fire). Available data suggested hydrologic impacts from the remnant rail grade but managers had insufficient quantitative data to assess these impacts. We initiated a fine scale assessment of topography, vegetation distribution, and hydrology to assess impacts from the remnant rail grade using lidar data, vegetation surveys, and piezometers. We developed topographic models, hydrological models, and mapped vegetation distribution. We developed statistical models to assess relationships between vegetation communities, hydrology, and distance to the rail grade. Surprisingly, we found that hydrologic flow paths did not conform to expectation and were not restricted by remnant land use features. For the most part, vegetation communities are responding to topographic and environmental gradients that existed prior to disturbance. Use of highly detailed topographic data (lidar), field hydrology, and vegetation studies allowed us to more accurately assess hydrologic and vegetation regimes, eliminating the need for mitigation, saving significant resources.

West Virginia↗