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Using assemblage data in ecological indicators: A comparison and evaluation of commonly available statistical tools

Ecological indicators are science-based tools used to assess how human activities have impacted environmental resources. For monitoring and environmental assessment, existing species assemblage data can be used to make these comparisons through time or across sites. An impediment to using assemblage data, however, is that these data are complex and need to be simplified in an ecologically meaningful way. Because multivariate statistics are mathematical relationships, statistical groupings may not make ecological sense and will not have utility as indicators. Our goal was to define a process to select defensible and ecologically interpretable statistical simplifications of assemblage data in which researchers and managers can have confidence. For this, we chose a suite of statistical methods, compared the groupings that resulted from these analyses, identified convergence among groupings, then we interpreted the groupings using species and ecological guilds. When we tested this approach using a statewide stream fish dataset, not all statistical methods worked equally well. For our dataset, logistic regression (Log), detrended correspondence analysis (DCA), cluster analysis (CL), and non-metric multidimensional scaling (NMDS) provided consistent, simplified output. Specifically, the Log, DCA, CL-1, and NMDS-1 groupings were ≥60% similar to each other, overlapped with the fluvial-specialist ecological guild, and contained a common subset of species. Groupings based on number of species (e.g., Log, DCA, CL and NMDS) outperformed groupings based on abundance [e.g., principal components analysis (PCA) and Poisson regression]. Although the specific methods that worked on our test dataset have generality, here we are advocating a process (e.g., identifying convergent groupings with redundant species composition that are ecologically interpretable) rather than the automatic use of any single statistical tool. We summarize this process in step-by-step guidance for the future use of these commonly available ecological and statistical methods in preparing assemblage data for use in ecological indicators.

Ecological Indicators↗

Emergent biogeochemical risks from Arctic permafrost degradation

The Arctic cryosphere is collapsing, posing overlapping environmental risks. In particular, thawing permafrost threatens to release biological, chemical and radioactive materials that have been sequestered for tens to hundreds of thousands of years. As these constituents re-enter the environment, they have the potential to disrupt ecosystem function, reduce the populations of unique Arctic wildlife and endanger human health. Here, we review the current state of the science to identify potential hazards currently frozen in Arctic permafrost. We also consider the cascading natural and anthropogenic processes that may compound the impacts of these risks, as it is unclear whether the highly adapted Arctic ecosystems have the resilience to withstand new stresses. We conclude by recommending research priorities to address these underappreciated risks.

Nature Climate Change↗

Land subsidence in the United States

This report explores the role of science in defining and understanding subsidence problems, and shows that the optimal use of our land and water resources may depend on improved scientific understanding to minimize subsidence. More than 80 percent of the identified land subsidence in the Nation is a consequence of human impact on subsurface water, and is an often overlooked environmental consequence of our land- and water-use practices. Nine illustrative case studies demonstrate the role of subsurface water in human-induced land subsidence. These studies represent three distinct processes that account for most of the water-related subsidence--compaction of aquifer systems, drainage and subsequent oxidation of organic soils, and dissolution and collapse of susceptible rocks. The compaction of alluvial aquifer systems that can accompany excessive ground-water pumping and resulting ground-water level declines is, by far, the single largest cause of subsidence.

Continental United States↗

Evolution of Ore Deposits and Technology Transfer Project: Isotope and Chemical Methods in Support of the U.S. Geological Survey Science Strategy, 2003-2008

Principal functions of the U.S. Geological Survey (USGS) Mineral Resources Program are providing assessments of the location, quantity, and quality of undiscovered mineral deposits, and predicting the environmental impacts of exploration and mine development. The mineral and environmental assessments of domestic deposits are used by planners and decisionmakers to improve the stewardship of public lands and public resources. Assessments of undiscovered mineral deposits on a global scale reveal the potential availability of minerals to the United States and other countries that manufacture goods imported to the United States. These resources are of fundamental relevance to national and international economic and security policy in our globalized world economy. Performing mineral and environmental assessments requires that predictions be made of the likelihood of undiscovered deposits. The predictions are based on geologic and geoenvironmental models that are constructed for the diverse types of mineral deposits from detailed descriptions of actual deposits and detailed understanding of the processes that formed them. Over the past three decades the understanding of ore-forming processes has benefited greatly from the integration of laboratory-based geochemical tools with field observations and other data sources. Under the aegis of the Evolution of Ore Deposits and Technology Transfer Project (referred to hereinafter as the Project), a 5-year effort that terminated in 2008, the Mineral Resources Program provided state-of-the-art analytical capabilities to support applications of several related geochemical tools to ore-deposit-related studies. The analytical capabilities and scientific approaches developed within the Project have wide applicability within Earth-system science. For this reason the Project Laboratories represent a valuable catalyst for interdisciplinary collaborations of the type that should be formed in the coming years for the United States to meet its natural-resources and natural-science needs. This circular presents an overview of the Project. Descriptions of the Project laboratories are given first including descriptions of the types of chemical or isotopic analyses that are made and the utility of the measurements. This is followed by summaries of select measurements that were carried out by the Project scientists. The studies are grouped by science direction. Virtually all of them were collaborations with USGS colleagues or with scientists from other governmental agencies, academia, or the private sector.

Circular↗

Widespread presence of naturally occurring perchlorate in high plains of Texas and New Mexico

Perchlorate (ClO4-) occurrence in groundwater has previously been linked to industrial releases and the historic use of Chilean nitrate fertilizers. However, recently a number of occurrences have been identified for which there is no obvious anthropogenic source. Groundwater from an area of 155 000 km2 in 56 counties in northwest Texas and eastern New Mexico is impacted by the presence of ClO4-. Concentrations were generally low (<4 ppb), although some areas are impacted by concentrations up to 200 ppb. ClO4- distribution is not related to well type (public water system, domestic, agricultural, or water-table monitoring) or aquifer (Ogallala, Edward Trinity High Plains, Edwards Trinity Plateau, Seymour, or Cenozoic). Results from vertically nested wells strongly indicate a surface source. The source of ClO4- appears to most likely be atmospheric deposition. Evidence supporting this hypothesis primarily relates to the presence of ClO 4- in tritium-free older water, the lack of relation between land use and concentration distribution, the inability of potential anthropogenic sources to account for the estimated mass of ClO4-, and the positive relationship between conserved anions (e.g., IO3-, Cl-, SO4-2) and ClO4-. The ClO4- distribution appears to be mainly related to evaporative concentration and unsaturated transport. This process has led to higher ClO4- and other ion concentrations in groundwater where the water table is relatively shallow, and in areas with lower saturated thickness. Irrigation may have accelerated this process in some areas by increasing the transport of accumulated salts and by increasing the number of evaporative cycles. Results from this study highlight the potential for ClO4- to impact groundwater in arid and semiarid areas through long-term atmospheric deposition. ?? 2006 American Chemical Society.

Environmental Science & Technology↗

Analysis of seafloor change around Dauphin Island, Alabama, 1987–2015

Dauphin Island is a 26-km-long barrier island located southwest of Mobile Bay, Alabama, in the north-central Gulf of Mexico. The island contains sandy beaches, dunes, maritime forests, freshwater ponds and intertidal wetlands, providing habitat for many endangered and threatened species. Dauphin Island also provides protection for and maintains estuarine conditions within Mississippi Sound, supporting oyster habitat and seagrasses. Wetland marshes along the Alabama mainland are protected by the island from wave-induced erosion during storms approaching from the Gulf of Mexico. Over the years, the island has been eroded by storms, most recently by Hurricane Ivan (2004) and Hurricane Katrina (2005) (Ivan/Katrina), which breached the island along its narrowest extent and caused damage to infrastructure. Along with storms producing significant episodic change, long-term beach erosion has exposed numerous pine tree stumps in the shoreface. The stumps are remnants of past maritime forests and reflect the consistent landward retreat of the island. Island change has prompted the State of Alabama to evaluate restoration alternatives to increase island resilience and sustainability by protecting and preserving the natural habitat, and by understanding the processes that influence shoreline change. Under a grant from the National Fish and Wildlife Foundation, restoration alternatives are being developed that will allow the State to make decisions on engineering and ecological restoration designs based on scientific analysis of likely outcomes and tradeoffs between impacts to stakeholder interests. Science-based assessment of the coastal zone requires accurate and up-to-date baseline data to provide a valid image of present conditions and to support modeling of coastal processes. Bathymetric elevation measurements are essential to this requirement. In August 2015, the U.S. Army Corps of Engineers and the U.S. Geological Survey conducted single beam and multibeam bathymetric surveys around Dauphin Island using a variety of shallow draft vessels and equipment. More than 95 square kilometers of seafloor was imaged. The data were integrated into a seamless digital elevation model to provide a high-resolution bathymetric map of the seafloor extending 9.5 kilometers seaward from the island’s eastern end and approximately 2 km along the rest of the island on the gulf and sound sides. Water depths range from 0.3 to 15.0 meters (m), with depths greater than 10.0 m constrained to the Mobile ship channel on the extreme eastern flank of the coverage. To measure seafloor change, two periods of historic hydrographic survey data were acquired from the National Oceanic and Atmospheric Administration National Centers for Environmental Information data archive. The two timeframes (1987–1988 and 2005–2007) were selected for their completeness of spatial coverage and because they encompass a period of significant storm impacts to the island. These timeframes were compared to each other and with the 2015 dataset to monitor elevation gain (sediment accretion) and elevation loss (sediment erosion) over time. Sediment dynamics is by far the most significant driver of nearshore elevation change in this area. The Mississippi-Alabama inner shelf is a passive margin, and other influences on elevation change (for example, tectonic adjustment, Holocene subsidence, and eustatic sea-level rise) are neither significant nor variable enough over this time period to have an imprint.

Alabama↗

Use of remote sensing techniques to determine the effects of grazing on vegetation cover and dune elevation at assateague island national seashore: Impact of horses

The effects of grazing by feral horses on vegetation and dune topography at Assateague Island National Seashore were investigated using color-infrared imagery, lidar surveys, and field measurements. Five pairs of fenced and unfenced plots (300 m2) established in 1993 on sand flats and small dunes with similar elevation, topography, and vegetation cover were used for this study. Color-infrared imagery from 1998 and field measurements from 2001 indicated that there was a significant difference in vegetation cover between the fenced and unfenced plot-pairs over the study period. Fenced plots contained a higher percentage of vegetation cover that was dominated by American beachgrass (Ammophila breviligulata). Lidar surveys from 1997, 1999, and 2000 showed that there were significant differences in elevation and topography between fenced and unfenced plot-pairs. Fenced plots were, on average, 0.63 m higher than unfenced plots, whereas unfenced plots had generally decreased in elevation after establishment in 1993. Results demonstrate that feral horse grazing has had a significant impact on dune formation and has contributed to the erosion of dunes at Assateague Island. The findings suggest that unless the size of the feral horse population is reduced, grazing will continue to foster unnaturally high rates of dune erosion into the future. In order to maintain the natural processes that historically occurred on barrier islands, much larger fenced exclosures would be required to prevent horse grazing. ?? 2004 Springer Science+Business Media, Inc.

Environmental Management↗

A multi-year comparison of IPCI scores for prairie pothole wetlands: implications of temporal and spatial variation

In the prairie pothole region of North America, development of Indices of Biotic Integrity (IBIs) to detect anthropogenic impacts on wetlands has been hampered by naturally dynamic inter-annual climate fluctuations. Of multiple efforts to develop IBIs for prairie pothole wetlands, only one, the Index of Plant Community Integrity (IPCI), has reported success. We evaluated the IPCI and its ability to distinguish between natural and anthropogenic variation using plant community data collected from 16 wetlands over a 4-year-period. We found that under constant anthropogenic influence, IPCI metric scores and condition ratings varied annually in response to environmental variation driven primarily by natural climate variation. Artificially forcing wetlands that occur along continuous hydrologic gradients into a limited number of discrete classes (e.g., temporary, seasonal, and semi-permanent) further confounded the utility of IPCI metrics. Because IPCI scores vary significantly due to natural climate dynamics as well as human impacts, methodology must be developed that adequately partitions natural and anthropogenically induced variation along continuous hydrologic gradients. Until such methodology is developed, the use of the IPCI to evaluate prairie pothole wetlands creates potential for misdirected corrective or regulatory actions, impairment of natural wetland functional processes, and erosion of public confidence in the wetland sciences.

Wetlands↗

Energy flow and the “grassification” of desert shrublands

In our directionally and continuously changing world, history still matters, and it does so in increasingly novel and important ways. Human adaptation to global change will rely heavily on robust baselines of historic environmental variability and detailed understanding of how both past and modern ecosystems have responded to both individual and multiple stressors. The question of global change has motivated an upsurge in paleoecological studies that span the late Quaternary and the modern era, and has inspired a growing consideration of time as a fundamental axis in ecology ( 1 ). A major challenge in developing pertinent ecological baselines remains how to fuse, into continuous time series, observations and experiments from living systems with paleoecological reconstructions from the same sites ( 2 , 3 ). Tracing and disentangling complex responses to environmental stress from paleological to present-day communities is especially daunting; for example, how climate change; accelerated land use; and biological invasions are influencing the flows of water, nutrients, and energy. The paper by Terry and Rowe in PNAS ( 4 ) is a shining example of how modern ecology and paleoecology can be spliced together to decipher how ecological processes unfold over time scales inaccessible to direct observation or experimentation, and how they can be disrupted by human impacts.

Proceedings of the National Academy of Sciences↗

6&6: A transdisciplinary approach to art-science collaboration

Despite an historical connection between the arts and sciences, in the past century, the two disciplines have been greatly siloed. However, there is a renewed interest in collaboration across the arts and sciences to support conservation practice by understanding and communicating complex environmental, social, and cultural challenges in novel ways. 6&6 was created as a transdisciplinary art–science initiative to promote a deeper appreciation of the Sonoran Desert. Six artists and six scientists were paired to create work that explored conservation issues in the Sonoran Desert and the Gulf of California. In-depth interviews were conducted with the artists and scientists throughout the 4-year initiative to understand the impact of 6&6 on their personal and professional behaviors and outlook. The findings from this case study reveal the role that intensive, place-based, and transdisciplinary art–science programs can play in shaping narratives to better communicate the patterns and processes of nature and human–environment interactions.

Arizona, Baja California, Baja California Sur, Cal↗

USGS environmental characterization of flood sediments left in the New Orleans area after Hurricanes Katrina and Rita, 2005 — Progress Report

Introduction: The flooding in the greater New Orleans area that resulted from Hurricanes Katrina and Rita in September, 2005, left behind accumulations of sediments up to many centimeters thick on streets, lawns, parking lots, and other flat surfaces. These flood sediment deposits have been the focus of extensive study by the US Environmental Protection Agency (EPA) and Louisiana Department of Environmental Quality (LDEQ) due to concerns that the sediments may contain elevated levels of heavy metals, organic contaminants, and microbes. The U.S. Geological Survey (USGS) is characterizing a limited number of flood sediment samples that were collected on September 15-16 and October 6-7, 2005, from the greater New Orleans area by personnel from the USGS Louisiana Water Science Center in Baton Rouge. Small samples (< 3 pints each) of wet to dry flood sediment were collected from 11 localities around downtown New Orleans on September 15, 2005, and two large samples (40 pints each) of wet flood sediment were collected from the Chalmette area on September 16. Twelve additional samples (8-10 pints each) were collected from New Orleans, Slidell, Rigolets, and Violet on October 6 and 7. The USGS characterization studies of these flood sediments are designed to produce data and interpretations regarding how the sediments and any contained contaminants may respond to environmental processes. This information will be of use to cleanup managers and DoI/USGS scientists assessing environmental impacts of the hurricanes and subsequent cleanup activities.

Louisiana↗

Land-Cover Trends of the Central Basin and Range Ecoregion

The U.S. Geological Survey (USGS) Land Cover Trends research project is focused on understanding the amounts, rates, trends, causes, and implications of contemporary land-use and land-cover (LU/LC) change in the United States. This project is supported by the USGS Geographic Analysis and Monitoring Program in collaboration with the U.S. Environmental Protection Agency (EPA) and the National Aeronautics and Space Administration (NASA). LU/LC change is a pervasive process that modifies landscape characteristics and affects a broad range of socioeconomic, biologic, and hydrologic systems. Understanding the impacts and feedbacks of LU/LC change on environmental systems requires an understanding of the rates, patterns, and driving forces of past, present, and future LU/LC change. The objectives of the Land Cover Trends project are to (1) determine and describe the amount, rates, and trends of contemporary LU/LC change by ecoregion for the period 1973-2000 for the conterminous United States, (2) document the causes, driving forces, and implications of change, and (3) synthesize individual ecoregion results into a national assessment of LU/LC change. The Land Cover Trends research team includes staff from the USGS National Center for Earth Resources Observation and Science (EROS), Rocky Mountain Geographic Science Center, Eastern Geographic Science Center, Mid-Continent Geographic Science Center, and the Western Geographic Science Center. Other partners include researchers at South Dakota State University, University of Southern Mississippi, and State University of New York College of Environmental Science and Forestry. This report presents an assessment of LU/LC change in the Central Basin and Range ecoregion for the period 1973-2000. The Central Basin and Range ecoregion is one of 84 Level-III ecoregions as defined by the Environmental Protection Agency. Ecoregions have served as a spatial framework for environmental resource management and to denote areas that contain a geographically distinct assemblage of biotic and abiotic phenomena including geology, physiography, vegetation, climate, soils, land use, wildlife, and hydrology. The established Land Cover Trends methodology generates estimates of LU/LC change using a probability sampling approach and change-detection analysis of thematic land-cover images derived from Landsat satellite imagery.

Scientific Investigations Report↗

Meeting the challenge of policy-relevant science: lessons from a water resource project

Water resource scientists face complex tasks in evaluating aspects of water projects, but relatively few assessment procedures have been applied and accepted as standard applications. Decision-makers often rely on environmental assessments to evaluate the value and operation of projects. There is often confusion about scientists' role in policy decisions. The scientist can affect policy-making as an expert withess, an advocate or a surrogate. By understanding the policy process, scientists can make their work more “policy relevant.” Using the Terror Lake hydro project in Alaska as a guide, three lessons are discussed: (1) not all problems are able to be solved with technology; (2) policy-relevant technology is rarely imposed on a problem; and (3) the scientist need not just react to the policy process, but can have an impact on how that process unfolds.

Journal of the American Water Resources Associatio↗

Deep-sea coral research and technology program: Alaska deep-sea coral and sponge initiative final report

Deep-sea coral and sponge ecosystems are widespread throughout most of Alaska’s marine waters. In some places, such as the central and western Aleutian Islands, deep-sea coral and sponge resources can be extremely diverse and may rank among the most abundant deep-sea coral and sponge communities in the world. Many different species of fishes and invertebrates are associated with deep-sea coral and sponge communities in Alaska. Because of their biology, these benthic invertebrates are potentially impacted by climate change and ocean acidification. Deepsea coral and sponge ecosystems are also vulnerable to the effects of commercial fishing activities. Because of the size and scope of Alaska’s continental shelf and slope, the vast majority of the area has not been visually surveyed for deep-sea corals and sponges. NOAA’s Deep Sea Coral Research and Technology Program (DSCRTP) sponsored a field research program in the Alaska region between 2012–2015, referred to hereafter as the Alaska Initiative. The priorities for Alaska were derived from ongoing data needs and objectives identified by the DSCRTP, the North Pacific Fishery Management Council (NPFMC), and Essential Fish Habitat-Environmental Impact Statement (EFH-EIS) process. This report presents the results of 15 projects conducted using DSCRTP funds from 2012-2015. Three of the projects conducted as part of the Alaska deep-sea coral and sponge initiative included dedicated at-sea cruises and fieldwork spread across multiple years. These projects were the eastern Gulf of Alaska Primnoa pacifica study, the Aleutian Islands mapping study, and the Gulf of Alaska fish productivity study. In all, there were nine separate research cruises carried out with a total of 109 at-sea days conducting research. The remaining projects either used data and samples collected by the three major fieldwork projects or were piggy-backed onto existing research programs at the Alaska Fisheries Science Center (AFSC).

NOAA Technical Memorandum↗

Local and regional factors affecting atmospheric mercury speciation at a remote location

Atmospheric concentrations of elemental (Hg0), reactive gaseous (RGM), and particulate (PHg) mercury were measured at two remote sites in the midwestern United States. Concurrent measurements of Hg0, PHg, and RGM obtained at Devil's Lake and Mt. Horeb, located approximately 65 km apart, showed that Hg0 and PHg concentrations were affected by regional, as well as local sources, while RGM was mainly impacted by local sources. Plumes reaching the Devil's Lake site from a nearby coal-fired power plant significantly impacted SO2 and RGM concentrations at Devil's Lake, but had little impact on Hg0. Our findings suggest that traditional modeling approaches to assess sources of mercury deposited that utilize source emissions and large-scale grids may not be sufficient to predict mercury deposition at sensitive locations due to the importance of small-scale sources and processes. We suggest the use of a receptor-based monitoring to better understand mercury source-receptor relationships.

Wisconsin↗

Nanomaterials in the environment: Behavior, fate, bioavailability, and effects—An updated review

The present review covers developments in studies of nanomaterials (NMs) in the environment since our much cited review in 2008. We discuss novel insights into fate and behavior, metrology, transformations, bioavailability, toxicity mechanisms, and environmental impacts, with a focus on terrestrial and aquatic systems. Overall, the findings were that: 1) despite substantial developments, critical gaps remain, in large part due to the lack of analytical, modeling, and field capabilities, and also due to the breadth and complexity of the area; 2) a key knowledge gap is the lack of data on environmental concentrations and dosimetry generally; 3) substantial evidence shows that there are nanospecific effects (different from the effects of both ions and larger particles) on the environment in terms of fate, bioavailability, and toxicity, but this is not consistent for all NMs, species, and relevant processes; 4) a paradigm is emerging that NMs are less toxic than equivalent dissolved materials but more toxic than the corresponding bulk materials; and 5) translation of incompletely understood science into regulation and policy continues to be challenging. There is a developing consensus that NMs may pose a relatively low environmental risk, but because of uncertainty and lack of data in many areas, definitive conclusions cannot be drawn. In addition, this emerging consensus will likely change rapidly with qualitative changes in the technology and increased future discharges.

Environmental Toxicology and Chemistry↗

Past abrupt changes, tipping points and cascading impacts in the Earth system

The geological record shows that abrupt changes in the Earth system can occur on timescales short enough to challenge the capacity of human societies to adapt to environmental pressures. In many cases, abrupt changes arise from slow changes in one component of the Earth system that eventually pass a critical threshold, or tipping point, after which impacts cascade through coupled climate–ecological–social systems. The chance of detecting abrupt changes and tipping points increases with the length of observations. The geological record provides the only long-term information we have on the conditions and processes that can drive physical, ecological and social systems into new states or organizational structures that may be irreversible within human time frames. Here, we use well-documented abrupt changes of the past 30 kyr to illustrate how their impacts cascade through the Earth system. We review useful indicators of upcoming abrupt changes, or early warning signals, and provide a perspective on the contributions of palaeoclimate science to the understanding of abrupt changes in the Earth system.

Nature Geoscience↗

Ecology and space: A case study in mapping harmful invasive species

The establishment and invasion of non-native plant species have the ability to alter the composition of native species and functioning of ecological systems with financial costs resulting from mitigation and loss of ecological services. Spatially documenting invasions has applications for management and theory, but the utility of maps is challenged by availability and uncertainty of data, and the reliability of extrapolating mapped data in time and space. The extent and resolution of projections also impact the ability to inform invasive species science and management. Early invasive species maps were coarse-grained representations that underscored the phenomena, but had limited capacity to direct management aside from development of watch lists for priorities for prevention and containment. Integrating mapped data sets with fine-resolution environmental variables in the context of species-distribution models allows a description of species-environment relationships and an understanding of how, why, and where invasions may occur. As with maps, the extent and resolution of models impact the resulting insight. Models of cheatgrass ( Bromus tectorum ) across a variety of spatial scales and grain result in divergent species-environment relationships. New data can improve models and efficiently direct further inventories. Mapping can target areas of greater model uncertainty or the bounds of modeled distribution to efficiently refine models and maps. This iterative process results in dynamic, living maps capable of describing the ongoing process of species invasions.

Book chapter↗