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Results for “Integrative Biology”

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At least 19 recordsLinked to original sources
USGS2019

Regional-scale associations between indicators of biological integrity and indicators of streamflow modification

Although streamflow is widely recognized as a controlling factor in stream health, empirical relations between indicators of anthropogenic modification of streamflow and ecological indicators have been elusive. The objective of this report is to build upon specific findings reported in recent publications by providing a library of empirical models that describe the relations between streamflow modification and indicators of biological integrity. Biological monitoring data from 812 streams and rivers across the United States were matched with sites where daily streamflow was also monitored by the U.S. Geological Survey. Of these sites, 118 were sampled by the U.S. Geological Survey along gradients of streamflow modification within 3 regional focus studies. The integrity of invertebrate and fish communities was expressed as a binary variable, “impaired” or “unimpaired,” signifying whether or not the composition and structure of the biological community was statistically reduced relative to regional reference sites. Streamflow modification at each gaged site was quantified with 509 streamflow statistics scaled to express the ratio of observed streamflow conditions to site-specific expected conditions in the absence of human influences on watershed hydrology. For each region, generalized additive modeling was used to examine relations between each indicator of streamflow modification and indicators of biological integrity (response variable). In every region examined, statistically defensible and ecologically realistic relations were found between indicators of streamflow modification and indicators of biological integrity. These findings can aid practitioners and managers seeking to (1) propose empirically based hypotheses about the specific components of streamflow regimes that are critical to aquatic communities, which can subsequently be explored in detail in a region or river basin of interest; and (2) predict biological responses to anthropogenic modification of specific components of the streamflow regime.

Open-File Report↗
USGS2002

An index of biological integrity for northern Mid-Atlantic Slope drainages

An index of biological integrity (IBI) was developed for streams in the Hudson, Delaware, and Susquehanna River drainages in the northeastern United States based on fish assemblage data from the Mohawk River drainage of New York. The original IBI, developed for streams in the U.S. Midwest, was modified to reflect the assemblage composition and structure present in Mid-Atlantic Slope drainages. We replaced several of the Midwestern IBI metrics and criteria scores because fishes common to the Midwest are absent from or poorly represented in the Northeast and because stream fish assemblages in the Northeast are less rich than those in the Midwest. For all replacement metrics we followed the ecology-based rationale used in the development of each of the metrics of the Midwestern IBI so that the basic theoretical underpinnings of the IBI remained unchanged. The validity of this modified IBI is demonstrated by examining the quality of streams in the Hudson, Delaware, and lower Susquehanna River basins. The relationships between the IBI and other indicators of environmental quality are examined using data on assemblages of fish and benthic macroinvertebrates and on chemical and physical stream characteristics obtained during 1993-2000 by the U.S. Geological Survey's National Water Quality Assessment Program in these three river basins. A principal components analysis (PCA) of chemical and physical variables from 27 sites resulted in an environmental quality gradient as the primary PCA axis (eigenvalue, 0.41 ). Principal components analysis site scores were significantly correlated with such benthic macroinvertebrate metrics as the percentage of Ephemeroptera, Plecoptera, and Trichoptera taxa (Spearman R = -0.66, P < 0.001). Index of biological integrity scores for sites in these three river basins were significantly correlated with this environmental quality gradient (Spearman R = -0.78, P = 0.0001). The northern Mid-Atlantic Slope IBI appears to be sensitive to environmental degradation in all three of the river basins addressed in this study. Adjustment of metric scoring criteria may be warranted, depending on composition of fish species in streams in the study area and on the relative effort used in the collection of fish assemblage data.

Transactions of the American Fisheries Society↗
USGS2022

Biology: Integrating core to essential variables (Bio-ICE) task team report for hard corals

The Interagency Ocean Observation Committee (IOOC) is chartered by the White House Office of Science and Technology Policy (OSTP) Subcommittee on Ocean Science and Technology (SOST). The purpose of the IOOC is to advise, assist, and make recommendations to the SOST on matters related to ocean observations via task teams such as the Biology - Integrating Core to Essential Variables (Bio-ICE) task team. The goal of the Bio-ICE task team is to advance the integration of biological observations from local, regional, and federal sources using best practices to inform national needs and ultimately feed seamlessly into the Global Ocean Observing System (GOOS), as appropriate. To accomplish this goal, and for the first time at the U.S. federal government level, a subgroup of the Bio-ICE task team focused on tropical, shallow-water (0-30 m) hard corals to identify commonalities between the U.S. Integrated Ocean Observing System (IOOS) core biological variable1 of “coral species and abundance,” the GOOS Essential Ocean Variable2 (EOV) “hard coral cover and composition,” the Group on Earth Observations Biological Observation Network (GEO BON) Essential Biodiversity Variables3 (EBVs), and the Global Climate Observing System (GCOS) Essential Climate Variables4 (ECVs) (Figure 1). The EOV data allows production of EBVs such as time series of maps of genetic composition, species populations, etc. Recognizing the complementarity of the different essential variable frameworks helps to promote best practices in observing and information management to facilitate data interoperability (Figure 1). The task team was charged with identifying where there are synergies in terms of spatial and temporal observing requirements and existing observation infrastructure and data delivery, including best practices and standard operating procedures. The task team also made suggestions to improve pathways for data flow for observations of these variables from Regional Associations of the U.S. IOOS, other nonfederal partners, and federal sources. The focus of the task team was on identifying and implementing best practices surrounding standardized data collection and data delivery to make continued progress toward adhering to the Findability, Accessibility, Interoperability, and Reuse (FAIR) and Collective benefit, Authority to control, Responsibility, and Ethics (CARE) data principles.

Task Team Report↗
USGS2015

A Candidate Vegetation Index of Biological Integrity Based on Species Dominance and Habitat Fidelity

Indices of biological integrity of wetlands based on vascular plants (VIBIs) have been developed in many areas of the USA and are used in some states to make critical management decisions. An underlying concept of all VIBIs is that they respond negatively to disturbance. The Ohio VIBI (OVIBI) is calculated from 10 metrics, which are different for each wetland vegetation class. We present a candidate vegetation index of biotic integrity based on floristic quality (VIBI-FQ) that requires only two metrics to calculate an overall score regardless of vegetation class. These metrics focus equally on the critical ecosystem elements of diversity and dominance as related to a species&rsquo; degree of fidelity to habitat requirements. The indices were highly correlated but varied among vegetation classes. Both indices responded negatively with a published index of wetland disturbance in 261 Ohio wetlands. Unlike VIBI-FQ, however, errors in classifying wetland vegetation may lead to errors in calculating OVIBI scores. This is especially critical when assessing the ecological condition of rapidly developing ecosystems typically associated with wetland restoration and creation projects. Compared to OVIBI, the VIBI-FQ requires less field work, is much simpler to calculate and interpret, and can potentially be applied to all habitat types. This candidate index, which has been &ldquo;standardized&rdquo; across habitats, would make it easier to prioritize funding because it would score the &ldquo;best&rdquo; and &ldquo;worst&rdquo; of all habitats appropriately and allow for objective comparison across different vegetation classes.

Ecological Indicators↗
USGS2010

The Index of Biological Integrity and the bootstrap revisited: an example from Minnesota streams

Multimetric indices, such as the Index of Biological Integrity (IBI), are increasingly used by management agencies to determine whether surface water quality is impaired. However, important questions about the variability of these indices have not been thoroughly addressed in the scientific literature. In this study, we used a bootstrap approach to quantify variability associated with fish IBIs developed for streams in two Minnesota river basins. We further placed this variability into a management context by comparing it to impairment thresholds currently used in water quality determinations for Minnesota streams. We found that 95% confidence intervals ranged as high as 40 points for IBIs scored on a 0&ndash;100 point scale. However, on average, 90% of IBI scores calculated from bootstrap replicate samples for a given stream site yielded the same impairment status as the original IBI score. We suggest that sampling variability in IBI scores is related to both the number of fish and the number of rare taxa in a field collection. A comparison of the effects of different scoring methods on IBI variability indicates that a continuous scoring method may reduce the amount of bias in IBI scores.

Minnesota↗
USGS2007

Developing terrestrial, multi-taxon indices of biological integrity: An example from coastal sage scrub

We screened 351 species or genera for their response to disturbance in coastal sage scrub (CSS) to develop a 15-metric, 5-taxon Index of Biological Integrity (IBI). We collected data on ants, birds, herpetofauna, small mammals, and plants for two years on 46 sites established across a gradient of disturbance in three reserves. The gradient spanned relatively intact CSS with thick stands of shrubs, to former CSS stands type-converted to exotic grasses. ANOVAs and clustering analyses indicated the IBI could distinguish four levels of disturbance in CSS. General measures of community structure, such as richness, did not show changes across the gradient for most taxa, and responses of taxa across the gradient were varied and rarely correlated. However, turnover in species or genera across the gradient was common across all taxa as shrub-obligate life forms were replaced by those favoring grassy or disturbed habitats. Our data indicate index-based approaches based on data collected across disturbance gradients may outperform more traditional community level metrics when responses to anthropogenic influences are complex and vary across species. ?? 2007 Elsevier Ltd. All rights reserved.

Biological Conservation↗
USGS1999

The use of aquatic macrophytes in monitoring and in assessment of biological integrity

Aquatic plant species, populations, and communities should be used as indicators of the aquatic environment, allowing detection of ecosystem response to different stressors. Plant tissues bioaccumulate and concentrate toxin levels higher than what is present in the sediments; and this appears to be related to organic matter content, acidification, and buffering capacity. The majority of toxicity studies, most of these with heavy metals, have been done with several Lemna species and Vallisneria americana. Organic chemicals reviewed include pesticides and herbicides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other industrial contaminants. The use of aquatic plant communities as bioindicators of environmental quality was evaluated for specific characteristics and indices that may assess biological integrity. Indices such as the floristic quality index (FQI) and coefficient of conservatism (C) are pioneering efforts to describe the quality of natural areas and protect native biodiversity. Our case study in the Grand Calumet Lagoons found that 'least-impacted' sites had the greatest aquatic plant species richness, highest FQI and C values, and highest relative abundance. Lastly, we introduce the concepts necessary for the development of a plant index of biotic integrity. Development of reference conditions is essential to understanding aquatic plant community structure, function, individual health, condition, and abundance. Information on guild development and tolerance definition are also integral to the development of a multi-metric index.

Book chapter↗
USGS2020

Identifying candidate reference reaches to assess the physical and biological integrity of wadeable streams in different ecoregions and among stream sizes

Efforts to quantify disturbances to aquatic systems often use landscape-level metrics, presumably linked to ecological integrity, but fewer studies have directly linked ecological integrity to instream habitat, and applied these results to unsampled stream reaches throughout a landscape. We developed a flexible, quantitative approach that characterizes stream impairment across a landscape and identifies least-disturbed stream reaches to serve as benchmarks for high quality physical habitat and ecological integrity. Fish and macroinvertebrate community characteristics, reach-level physical habitat and water quality metrics were summarized in 891 wadeable stream reaches across two ecoregions in Missouri, USA. The influence of reach and water-quality characteristics as well as landscape-level variables on 7 fish and 3 macroinvertebrate community biological indicator metrics was then modeled using boosted regression trees (BRTs). On average, reach-level models explained more variance (25 and 27% in the two ecoregions examined) in biotic metrics than landscape-level models (18% and 20%). Abiotic and biotic associations differed among ecoregions and stream sizes, however, reach-level habitat (e.g., bankfull width/depth ratio, channel incision height) and water quality (e.g., dissolved oxygen, total chlorophyll) were consistently top predictors. At the landscape scale, fish richness in the agriculturally dominated ecoregion increased with decreased fragmentation/flow modification, while invertebrate metrics responded to agricultural disturbances. Invertebrate metrics in the forested ecoregion showed community degradation apparent with crop coverage as low as 8-10% of the riparian zone, while urban impairment was best detected using invertebrate indicators of biotic integrity and measures of fish trophic ecology. Relationships among landscape-scale variables and reach characteristics identified as top predictors in BRTs also highlighted potential mechanistic relationships among landscape, habitat, and measures of ecological integrity. Using the results of the landscape-level models, estimates for overall ecological integrity were predicted for over 28,000 stream reaches throughout Missouri, and a total of 1,423 candidate reference reaches were identified. The objective approach to characterizing stream impairment developed in this study offers specific advantages, including a reach and landscape-level evaluation of human disturbance as well as an inductive, multi-metric determination of ecological integrity.

Missouri↗
USGS2022

Biology: Integrating core to essential variables (Bio-ICE) task team report for marine mammals

Marine mammals are wide-ranging, relatively long-lived organisms that play a crucial role in maintaining healthy ocean ecosystems. Often referred to as ecosystem engineers and sentinel species in marine ecosystems, these charismatic megafauna feed at a variety of trophic levels, affecting food web dynamics and cycling of chemicals and nutrients in the water column as well as in benthic habitats, both nearshore and in the deep ocean. An understanding of their abundance and distribution is an essential starting point for evaluating their role in ocean ecosystems. Accordingly, marine mammals have been included among key variables to monitor in ocean observing systems, from core variables for the U.S. Integrated Ocean Observing System (IOOS) to an Essential Ocean Variable (EOV) for the Global Ocean Observing System (GOOS). They also contribute to several Essential Biodiversity Variables (EBVs) for the Group on Earth Observations Biodiversity Observation Network (GEO BON). Further, evaluation of the health of marine mammal populations will help deliver societal benefits by contributing to the UN Decade of Ocean Science for Sustainable Development; informing reporting activities such as the World Ocean Assessment; and supporting achievement of Sustainable Development Goal 14, the post-2020 framework for the Convention for Biological Diversity, and a new treaty for conservation and sustainable use of marine biodiversity beyond national jurisdiction. In the U.S., the National Marine Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (FWS) are required to produce stock assessments for marine mammals under the Marine Mammal Protection Act (MMPA, 16 U.S.C. §1371 et seq.). Stock assessment analyses require accurate, up to-date information on abundance and distribution to inform appropriate management and/or conservation measures. Despite the availability of information on abundance and distribution within the stock assessment reports, availability and accessibility of the underlying data to the broader ocean observing community and contribution to EOVs remain inconsistent.

Report↗
USGS2003

An index of biological integrity (IBI) for Pacific Northwest rivers

The index of biotic integrity (IBI) is a commonly used measure of relative aquatic ecosystem condition; however, its application to coldwater rivers over large geographic areas has been limited. A seven-step process was used to construct and test an IBI applicable to fish assemblages in coldwater rivers throughout the U.S. portion of the Pacific Northwest. First, fish data from the region were compiled from previous studies and candidate metrics were selected. Second, reference conditions were estimated from historical reports and minimally disturbed reference sites in the region. Third, data from the upper Snake River basin were used to test metrics and develop the initial index. Fourth, candidate metrics were evaluated for their redundancy, variability, precision, and ability to reflect a wide range of conditions while distinguishing reference sites from disturbed sites. Fifth, the selected metrics were standardized by being scored continuously from 0 to 1 and then weighted as necessary to produce an IBI ranging from 0 to 100. The resulting index included 10 metrics: number of native coldwater species, number of age-classes of sculpins Cottus spp., percentage of sensitive native individuals, percentage of coldwater individuals, percentage of tolerant individuals, number of alien species, percentage of common carp Cyprinus carpio individuals, number of selected salmonid age-classes, catch per unit effort of coldwater individuals, and percentage of individuals with selected anomalies. Sixth, the IBI responses were tested with additional data sets from throughout the Pacific Northwest. Last, scores from two minimally disturbed reference rivers were evaluated for longitudinal gradients along the river continuum. The IBI responded to environmental disturbances and was spatially and temporally stable at over 150 sites in the Pacific Northwest. The results support its use across a large geographic area to describe the relative biological condition of coolwater and coldwater rivers with low species richness.

Transactions of the American Fisheries Society↗
USGS2016

Integrating biology, field logistics, and simulations to optimize parameter estimation for imperiled species

Conservation of imperiled species often requires knowledge of vital rates and population dynamics. However, these can be difficult to estimate for rare species and small populations. This problem is further exacerbated when individuals are not available for detection during some surveys due to limited access, delaying surveys and creating mismatches between the breeding behavior and survey timing. Here we use simulations to explore the impacts of this issue using four hypothetical boreal toad ( Anaxyrus boreas boreas ) populations, representing combinations of logistical access (accessible, inaccessible) and breeding behavior (synchronous, asynchronous). We examine the bias and precision of survival and breeding probability estimates generated by survey designs that differ in effort and timing for these populations. Our findings indicate that the logistical access of a site and mismatch between the breeding behavior and survey design can greatly limit the ability to yield accurate and precise estimates of survival and breeding probabilities. Simulations similar to what we have performed can help researchers determine an optimal survey design(s) for their system before initiating sampling efforts.

Ecological Modelling↗
USGS2011

Impacts of agricultural land use on biological integrity: A causal analysis

Agricultural land use has often been linked to nutrient enrichment, habitat degradation, hydrologic alteration, and loss of biotic integrity in streams. The U.S. Geological Survey's National Water Quality Assessment Program sampled 226 stream sites located in eight agriculture‐dominated study units across the United States to investigate the geographic variability and causes of agricultural impacts on stream biotic integrity. In this analysis we used structural equation modeling (SEM) to develop a national and set of regional causal models linking agricultural land use to measured instream conditions. We then examined the direct, indirect, and total effects of agriculture on biotic integrity as it acted through multiple water quality and habitat pathways. In our nation‐wide model, cropland affected benthic communities by both altering structural habitats and by imposing water quality‐related stresses. Region‐specific modeling demonstrated that geographic context altered the relative importance of causal pathways through which agricultural activities affected stream biotic integrity. Cropland had strong negative total effects on the invertebrate community in the national, Midwest, and Western models, but a very weak effect in the Eastern Coastal Plain model. In the Western Arid and Eastern Coastal Plain study regions, cropland impacts were transmitted primarily through dissolved water quality contaminants, but in the Midwestern region, they were transmitted primarily through particulate components of water quality. Habitat effects were important in the Western Arid model, but negligible in the Midwest and Eastern Coastal Plain models. The relative effects of riparian forested wetlands also varied regionally, having positive effects on biotic integrity in the Eastern Coastal Plain and Western Arid region models, but no statistically significant effect in the Midwest. These differences in response to cropland and riparian cover suggest that best management practices and planning for the mitigation of agricultural land use impacts on stream ecosystems should be regionally focused.

Ecological Applications↗
USGS1998

Application of an index of biotic integrity for dunal, palustrine wetlands: Emphasis on assessment of nonpoint source landfill effects on the Grand Calumet Lagoons

Using a newly modified index of biotic integrity for assessing biological integrity of fish communities in dunal, palustrine wetlands, we assessed the non-point source influence of an industrial landfill on the Grand Calumet Lagoons. The landfill is primarily an iron and steel manufacturer's slag waste. No sensitive species, hybrids, headwater species, and either few or no simple lithophilic spawning species were collected from any of the sites in the Grand Calumet Lagoons. Species catch-per-unit of effort varied significantly between reaches in the Middle Lagoon and the West Lagoon. The most disturbed areas were adjacent to the industrial landfill and along the southern shore near the outflow from the West Lagoon. Near- and far-field stations possessed similar numbers of species and relative abundance. The near-field stations showed an increase in tolerant species, a higher proportion of omnivores and carnivores, and a lower environmental quality rating of ‘poor-very poor’. The far-field sites were classified as having ‘fair’ biological integrity and showed an increase in relative abundance, proportion of sensitive species, and an increase in simple lithophils. The loss of biological integrity in the West Pond was not accurately predicted using the modified index of biotic integrity, even though it was rated as extremely degraded by the biological diversity indices. Fish communities were negatively impacted by proximity to the landfill.

Indiana↗
USGS2001

Influence of stream habitat and land use on benthic macroinvertebrate indicators of stream quality of selected above-tidal streams in the Houston-Galveston Area Council service area, Texas, 1997–98

During 1997–98, the U.S. Geological Survey, in cooperation with the Houston-Galveston Area Council, collected stream-habitat and benthic macroinvertebrate data for 31 reaches on abovetidal streams in the Council service area near Houston, Texas. Stream-habitat, land-use and population, and benthic aquatic insect metrics were determined for the 31 reaches. Statistical analyses were used to determine the stream-habitat, land-use and population, and aquatic insect variables that are strongly intercorrelated and that explain the greatest amount of variation between the reaches. Comparison of stream-habitat and biological integrity scores computed for each of the 31 reaches indicated (1) reaches generally had larger stream-habitat integrity scores in drainage areas that were heavily forested and had fewer people per square mile, (2) larger biological integrity scores were significantly correlated with larger stream-habitat integrity scores, and (3) urban reaches generally had more simplified streamhabitat conditions and smaller biological integrity scores. Seven reaches in the study area were selected as reference reaches on the basis of high streamhabitat integrity and high biological integrity. The reference-reaches median biological integrity score was equaled or exceeded by three reaches (one on Spring Creek and two on Cypress Creek) that are on the State of Texas 303(d) list of threatened or impaired waters with respect to aquatic life. This indicates that direct measures of biological integrity could be used to supplement surrogatebased designations of biological integrity such as the State list. A statistically significant multipleregression model was developed that uses independent variables that can be obtained without fieldintensive studies to predict the biological integrity score for a reach. The deviation from the model’s predicted score with the score based on biological sampling can be used to interpret the degree of biological impairment in a reach. Data from reaches outside the group of reaches used in this study are needed to test the validity of the multipleregression model.

Texas↗
USGS2013

Disturbance metrics predict a wetland Vegetation Index of Biotic Integrity

Indices of biological integrity of wetlands based on vascular plants (VIBIs) have been developed in many areas in the USA. Knowledge of the best predictors of VIBIs would enable management agencies to make better decisions regarding mitigation site selection and performance monitoring criteria. We use a novel statistical technique to develop predictive models for an established index of wetland vegetation integrity (Ohio VIBI), using as independent variables 20 indices and metrics of habitat quality, wetland disturbance, and buffer area land use from 149 wetlands in Ohio, USA. For emergent and forest wetlands, predictive models explained 61% and 54% of the variability, respectively, in Ohio VIBI scores. In both cases the most important predictor of Ohio VIBI score was a metric that assessed habitat alteration and development in the wetland. Of secondary importance as a predictor was a metric that assessed microtopography, interspersion, and quality of vegetation communities in the wetland. Metrics and indices assessing disturbance and land use of the buffer area were generally poor predictors of Ohio VIBI scores. Our results suggest that vegetation integrity of emergent and forest wetlands could be most directly enhanced by minimizing substrate and habitat disturbance within the wetland. Such efforts could include reducing or eliminating any practices that disturb the soil profile, such as nutrient enrichment from adjacent farm land, mowing, grazing, or cutting or removing woody plants.

Ecological Indicators↗
USGS2004

National Wildlife Refuge System: Ecological context and integrity

The Refuge Improvement Act of 1997 established a statutory mission and management standards for the National Wildlife Refuge system. The U.S. Fish and Wildlife Service subsequently issued a policy for ensuring the biological integrity, diversity, and environmental health of the system. This policy requires understanding the management objectives of each refuge in a local, regional, and national context. An assessment of the refuge system in a national and regional context reveals that refuges are typically smaller than many conservation holdings and are unevenly distributed across the conterminous U.S. Western rangelands, coastal wetlands, and northern grasslands; wetlands are the best-represented ecosystems, while temperate forests have the poorest representation. In contrast to other agency holdings or management designations in the national protected areas network (e.g., national parks, national forests, wilderness areas), refuges tend to occupy sites at lower elevations and that have higher productivity and soil quality. This difference points to the important contribution of the refuges in providing much needed ecological balance within the national protected areas network. However, the ecological integrity of the refuge system is challenged by the proximity of individual refuges to development. Overall, the refuges are becoming islands in a landscape matrix of urban and agricultural development. This creates future challenges for meeting management objectives to ensure the biological integrity, diversity, and environmental health of the system. If the policy to ensure biological integrity, diversity, and environmental health of the refuge system is to be successful, it may be more important to address issues about what happens on adjacent lands than uses within refuges.

Natural Resources Journal↗