Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Integrative Biology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources
USGS2026

Biome-scale spatial patterns of avian abundance reveal proactive conservation opportunities in North American grasslands

North American grassland birds have experienced steeper population declines than any other avian guild, yet conservation efforts remain largely reactive and fragmented. We used nearly four decades of North American Breeding Bird Survey data to identify biome-scale spatial patterns (clustering) of grassland bird abundance for the Great Plains. Our results reveal an ecological core in the north-central Plains where community-level abundance is either increasing by >100% or remains high and stable, providing a strategic roadmap for a “Defend the Core” conservation approach. This approach flips the script from reactive triage centered on isolated population fragments to a proactive strategy of maintaining large-scale ecosystem integrity. Conversely, we found that population losses are more spatially clustered than wins, reflecting the relentless, one-way movement of woody encroachment and agricultural conversion. This asymmetry supports prioritizing intact landscapes, as current restoration rates are often outpaced by the scale of habitat loss. Notably, we found that community-level spatial clustering is a more robust indicator of biome condition than trends of individual flagship species, suggesting that managing for ecosystem integrity provides a more effective multi-species umbrella. Given our results, there is an opportunity for operationalizing a Great Plains Conservation Design that is ecosystem-centric and rooted in the sustainability of the private-land cattle production that maintains these open spaces. By leveraging avian abundance as a biological sensor, managers and producers can deploy a shared vision that matches the spatial scale of the threats, moving from reactive triage to proactive defense of core working grasslands in North America.

Great Plains biome↗
USGS2015

Southern Salish Sea Habitat Map Series: Admiralty Inlet

In 2010 the Environmental Protection Agency, Region 10 initiated the Puget Sound Scientific Studies and Technical Investigations Assistance Program, designed to support research in support of implementing the Puget Sound Action Agenda. The Action Agenda was created in response to Puget Sound having been designated as one of 28 estuaries of national significance under section 320 of the U.S. Clean Water Act, and its overall goal is to restore the Puget Sound Estuary's environment by 2020. The Southern Salish Sea Mapping Project was funded by the Assistance Program request for proposals process, which also supports a large number of coastal-zone- and ocean-management issues. The issues include the recommendations of the Marine Protected Areas Work Group to the Washington State Legislature (Van Cleve and others, 2009), which endorses a Puget Sound and coast-wide marine conservation needs assessment, gap analysis of existing Marine Protected Areas (MPA) and recommendations for action. This publication is the first of four U.S. Geological Survey Scientific Investigation Maps that make up the Southern Salish Sea Mapping Project. The remaining three map blocks to be published in the future, located south of Admiralty Inlet, are shown in figure 1. Puget Sound is a deep, fjord-type estuary covering an area of 2,330 km 2 in the Pacific Northwest region of the United States (fig. 1). It is connected to the ocean by the Strait of Juan de Fuca, a turbulent passage approximately 160 km in length and 22 km wide at its west end, expanding to over 40 km wide at its east end (Thomson, 1994). During the Pleistocene, the area was occupied several times by lobes of continental ice, resulting in a complex basin-fill of glacial and interglacial deposits that are locally as thick as 1100 m (Johnson and others, 2001). The last glaciation, called the Fraser glaciation, began after 28,800±740 14 C yr B.P. when ice started a slow expansion (Clague, 1981). At peak advance the westward Juan de Fuca lobe reached the edge of the continental shelf through the Juan de Fuca Strait shortly before 14,460±200 14 C yr B.P. (Herzer and Bornhold, 1982). The southward Puget lobe advanced to its terminal position in Puget Sound by around 14,150 14 C yr B.P. (Porter and Swanson, 1998). Ice retreated from its maximum to northern Whidbey Island by 13,650±350 14 C yr B.P. (Dethier and others, 1995). Retreating glaciers resulted in a thick sequence of ice-contact, glacial-marine sediment, and early post-glacial sediments (Linden and Schurrer, 1988). These deposits have experienced the effects of a marine transgression followed by regression, resulting in a sea-level several tens of meters lower than the present day (Linden and Schurrer, 1988). A second transgression brought sea level to about the present level by around 5,470±120 14 C yr B.P. (Clague and others, 1982) establishing the present oceanographic and geologic environment Puget Sound is separated into four interconnected basins; Whidbey, Central (Main), Hood Canal, and South (Thomson, 1994). The Whidbey, Central, and Hood Canal basins are the three main branches of the Puget Sound estuary and are separated from the Strait of Juan de Fuca by a double sill at Admiralty Inlet. The Admiralty Inlet map area includes the Inlet and a portion of the Whidbey Basin (fig. 1). The shallower South Basin is separated by a sill at Tacoma Narrows and is highly branched with numerous finger inlets. Flow within Puget Sound is dominated by tidal currents of as much as 1 m/s at Admiralty Inlet, reducing to approximately 0.5 m/s in the Central Basin (Lavelle and others, 1988). The lack of silt and clay-sized sediments in the Admiralty Inlet map area is likely a result of the strong currents (see Ground-Truth Studies for the Admiralty Inlet Map Area, sheet 3). The subtidal component of flow reaches approximately 0.1 m/s and is driven by density gradients arising from the contrast in salty ocean water at the entrance and freshwater inputs from stream flow (Lavelle and others, 1988). The total freshwater input to Puget Sound is approximately 3.4 x 10 6 m 3 /day, primarily from the Skagit River (Cannon, 1983). The subtidal circulation mostly consists of a two-layered flow in the basins with fresher water exiting at the surface and saltier water entering at depth (Ebbesmeyer and Cannon, 2001). In general, surface waters flow north and deeper waters flow south; variations arise from wind effects that can drive a surface current in the same direction as the wind, and a baroclinic response in the lower layer to about 100-m depth (Matsuura and Cannon, 1997). Oceanographic properties are influenced by temporal forcing parameters such as reduced stream flow during the 2000-01 drought that increased surface salinity and decreased differences between surface and bottom waters (Newton and others, 2003). On offshore seismic-reflection profiles, Pleistocene strata (excluding latest Pleistocene glacial and post-glacial deposits) form a distinct seismic unit, bounded below by pre-Tertiary or Tertiary basement and above by typically flat-lying latest Pleistocene to Holocene deposits that fill in erosional or depositional relief (Johnson and others, 2001). Cores from central Puget Sound have accumulation rates that range from 85 to 1200 mg/cm 2 /yr, or 0.12 to 2.4 cm/yr; the highest accumulation rates are near the southern end of central Puget Sound (Carpenter and others, 1985). Carpenter and others (1985) un-weighted arithmetic mean of accumulation rates for central Puget Sound deeper stations is 480±340 (± one standard deviation) mg/cm 2 /yr. Lavelle and others (1985) also found rates as high as 1200 mg/cm 2 /yr over the past approximately 70 years in cores in the Central Basin off of and north and south of Elliott Bay. Puget Sound basin rates are comparable to rates in midshelf silt deposits on the Washington coast north of the Columbia River (Nittrouer and others, 1979). The deep subtidal (in other words, below SCUBA depths) habitats of Puget Sound are relatively poorly known. A few subtidal surveys exist for several habitat types from the 1960s and 1970s (reviewed in Dethier, 1990), using grab and box core data. The Dethier (1990) review divides habitat up into Coast and Marine Ecological Classification Standard (CMECS) substrate, water column energy, and depth zones but does not attempt to map these habitats, rather it is an inventory of habitats found in the area and the flora and fauna associated with each habitat. The approach of the Southern Salish Sea Mapping project is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data (the undersea equivalent of satellite remote-sensing data in terrestrial mapping), acoustic backscatter, seafloor video, seafloor photography, and bottom-sediment sampling data. This approach is based in part on methods presented and data collection and product needs identified at the Washington State Seafloor Mapping Workshop (Washington State Seafloor Mapping Workshop Steering Committee, 2008), attended by coastal and marine managers and scientists. The map products display seafloor geomorphology and substrate, and identify potential marine benthic habitats. It is emphasized that the more interpretive habitat and geology maps rely on the integration of multiple, new high-resolution datasets and that mapping at small scales would not be possible without such data. Oceanographic current and wave data is not included in this analysis, however, the accompanying geographic information system (GIS) data set is designed and intended to be combined with oceanographic and biologic data sets assembled by others in the future and some of the GIS data has already been incorporated in the unpublished Nature Conservancy Benthic Habitats of Puget Sound database. This publication includes four map sheets, explanatory text, and a descriptive pamphlet. Each map sheet is published as a portable document format (PDF) file. ESRI ArcGIS compatible geotiffs (for example, bathymetry) and shapefiles (for example video observation points) will be available for download in the data catalog associated with this publication (Cochrane, 2015). An ArcGIS Project File with the symbology used to generate the map sheets is also provided. For those who do not own the full suite of ESRI GIS and mapping software, the data can be read using ESRI ArcReader, a free viewer that is available at http://www.esri.com/software/arcgis/arcreader/index.html .

Washington↗
USGS2002

Analysis and Management of Animal Populations: Modeling, Estimation and Decision Making

This book deals with the processes involved in making informed decisions about the management of animal populations. It covers the modeling of population responses to management actions, the estimation of quantities needed in the modeling effort, and the application of these estimates and models to the development of sound management decisions. The book synthesizes and integrates in a single volume the methods associated with these themes, as they apply to ecological assessment and conservation of animal populations. KEY FEATURES * Integrates population modeling, parameter estimation and * decision-theoretic approaches to management in a single, cohesive framework * Provides authoritative, state-of-the-art descriptions of quantitative * approaches to modeling, estimation and decision-making * Emphasizes the role of mathematical modeling in the conduct of science * and management * Utilizes a unifying biological context, consistent mathematical notation, * and numerous biological examples

Book↗
USGS2000

The National Biological Information Infrastructure: Coming of age

Coordinated by the US Geological Survey, the National Biological Information Infrastructure (NBII) is a Web-based system that provides increased access to data and information on the nation's biological resources. The NBII can be viewed from a variety of perspectives. This article - an individual case study and not a broad survey with extensive references to the literature - addresses the structure of the NBII related to thematic sections, infrastructure sections and place-based sections, and other topics such as the Integrated Taxonomic Information System (one of our more innovative tools) and the development of our controlled vocabulary.

Online and CDROM Review↗
USGS2017

Community distance sampling models allowing for imperfect detection and temporary emigration

Recent developments of community abundance models (CAMs) enable us to analyze communities subject to imperfect detection. However, existing CAMs assume spatial closure, that is, that individuals are always present in the sampling plots, which is often violated in field surveys. Violation of this assumption, such as in the presence of spatial temporary emigration, can lead to the underestimates of detection probability and overestimates of population densities and diversity metrics. Here, we propose a model that simultaneously accommodates both temporary emigration and imperfect detection by integrating CAMs and a form of hierarchical distance sampling for open populations. Expected values of species richness are obtained via the summation of occupancy (or incidence) probabilities, based on species‐level densities, across all species of the community. Simulations were used to examine the effects of spatial temporary emigration on the estimation of biological communities. We also applied the proposed model to empirical data and constructed area‐based rarefaction curves accounting for temporary emigration. Simulation experiments showed that temporary emigration can decrease the local species richness (α diversity) based on densities and increase the species turnover (β diversity). Raw species counts can overestimate or underestimate α diversity in the presence of temporary emigration, but the specific biases depend on the values of detection and emigration probabilities. Our newly proposed model yielded unbiased estimates of α, β, and γ diversity in the presence of temporary emigration. The application to empirical data suggested that accounting for temporary emigration lowered area‐based rarefaction curves because availability probabilities of individual species were estimated to be <1. Temporary emigration prevails in field surveys and has broad significance for understanding the ecology and function of biological communities and separation of imperfect detection and temporary emigration resolves long‐standing issues in the use of count data. We therefore suggest that the consideration of temporary emigration would contribute to understanding the nature and role of biological communities.

Ecosphere↗
USGS2021

Multiple lines of evidence for identifying potential hazards to fish from contaminants of emerging concern in Great Lakes tributaries

Contaminants of emerging concern (CECs; e.g., pharmaceuticals, flame retardants, pesticides, and industrial chemicals) are omnipresent throughout tributaries to the Great Lakes. Furthermore, CECs are often present at concentrations that are potentially hazardous to aquatic species. Since 2010, we characterized the presence of CECs at 309 sites within 47 Great Lakes tributaries and characterized responses of fathead minnow ( Pimephales promelas ) exposed to river water at a subset of 26 sites within four tributaries. Our work resulted in three independent lines of evidence related to the potential hazards of CEC exposure to fish. First, vulnerability (where vulnerability refers to likelihood) of surface waters to CEC presence was predicted using select watershed characteristics. Second, hazard to fish (where hazard means the potential for adverse biological responses) was predicted using screening values for a subset of CECs. Third, biological responses of fathead minnow exposed to river water in streamside exposures were measured. We assessed the congruence of these three lines of evidence for identifying sites with elevated hazards to CEC exposure. Predicted vulnerability and hazards agreed at 66% of all sites. Where the two indices did not agree, vulnerability often underestimated predicted hazard. When compared with measured biological responses from streamside exposures, predicted hazards agreed for 42% of samples. Furthermore, when predicted hazards for specific effect categories were compared with similar measured biomarkers, 26% and 46% of samples agreed for reproductive and physiological effect categories, respectively. Overall, vulnerability and hazard predictions tended to overestimate the measured biological responses, providing a protective estimate of the potential hazards of CEC exposure to fish. When used together, these three approaches can help resource managers prioritize management activities in minimizing hazards of CEC exposure and can be used by researchers to prioritize studies focused on understanding the hazards of CEC exposure to fish. Integr Environ Assess Manag 2022;18:1246–1259. © 2021 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Great Lakes↗
USGS2007

Chapter 8 Tool for monitoring hydrophilic contaminants in water: polar organic chemical integrative sampler (POCIS)

The development of the polar organic chemical integrative sampler (POCIS) provides environmental scientists and policy makers a tool for assessing the presence and potential impacts of the hydrophilic component of these organic contaminants. The POCIS provides a means for determining the time-weighted average (TWA) concentrations of targeted chemicals that can be used in risk assessments to determine the biological impact of hydrophilic organic compounds (HpOCs) on the health of the impacted ecosystem. Field studies have shown that the POCIS has advantages over traditional sampling methods in sequestering and concentrating ultra-trace to trace levels of chemicals over time resulting in increased method sensitivity, ability to detect chemicals with a relatively short residence time or variable concentrations in the water, and simplicity in use. POCIS extracts can be tested using bioassays and can be used in organism dosing experiments for determining toxicological significance of the complex mixture of chemicals sampled. The POCIS has been successfully used worldwide under various field conditions ranging from stagnant ponds to shallow creeks to major river systems in both fresh and brackish water.

Comprehensive Analytical Chemistry↗
USGS2014

A multiscale, hierarchical model of pulse dynamics in arid-land ecosystems

Ecological processes in arid lands are often described by the pulse-reserve paradigm, in which rain events drive biological activity until moisture is depleted, leaving a reserve. This paradigm is frequently applied to processes stimulated by one or a few precipitation events within a growing season. Here we expand the original framework in time and space and include other pulses that interact with rainfall. This new hierarchical pulse-dynamics framework integrates space and time through pulse-driven exchanges, interactions, transitions, and transfers that occur across individual to multiple pulses extending from micro to watershed scales. Climate change will likely alter the size, frequency, and intensity of precipitation pulses in the future, and arid-land ecosystems are known to be highly sensitive to climate variability. Thus, a more comprehensive understanding of arid-land pulse dynamics is needed to determine how these ecosystems will respond to, and be shaped by, increased climate variability.

Annual Review of Ecology, Evolution, and Systemati↗
USGS2020

Benthic habitat is an integral part of freshwater Mysis ecology

Diel vertical migration (DVM) is common in aquatic organisms. The trade‐off between reduced predation risk in deeper, darker waters during the day and increased foraging opportunities closer to the surface at night is a leading hypothesis for DVM behaviour. Diel vertical migration behaviour has dominated research and assessment frameworks for Mysis , an omnivorous mid‐trophic level macroinvertebrate that exhibits strong DVM between benthic and pelagic habitats and plays key roles in many deep lake ecosystems. However, some historical literature and more recent evidence indicate that mysids also remain on the bottom at night, counter to expectations of DVM. We surveyed the freshwater Mysis literature using Web of Science (WoS; 1945–2019) to quantify the frequency of studies on demographics, diets, and feeding experiments that considered, assessed, or included Mysis that did not migrate vertically but remained in benthic habitats. We supplemented our WoS survey with literature searches for relevant papers published prior to 1945, journal articles and theses not listed in WoS, and additional references known to the authors but missing from WoS (e.g. only 47% of the papers used to evaluate in situ diets were identified by WoS). Results from the survey suggest that relatively little attention has been paid to the benthic components of Mysis ecology. Moreover, the literature suggests that reliance on Mysis sampling protocols using pelagic gear at night provides an incomplete picture of Mysis populations and their role in ecosystem structure and function. We summarise current knowledge of Mysis DVM and provide an expanded framework that more fully considers the role of benthic habitat. Acknowledging benthic habitat as an integral part of Mysis ecology will enable research to better understand the role of Mysis in food web processes.

Freshwater Biology↗
USGS2007

Factors affecting the reproduction, recruitment, habitat, and population dynamics of pallid sturgeon and shovelnose sturgeon in the Missouri River

For more than a hundred years, human activities have modified the natural forces that control the Missouri River and its native fish fauna. While the ecological effects of regulation and channel engineering are understood in general, the current understanding is not sufficient to guide river restoration and management. The U.S. Geological Survey (USGS) is in the third year of a multiagency research effort to determine the ecological requirements for reproduction and survival of the endangered pallid sturgeon (Scaphirhynchus albus) and shovelnose sturgeon (Scaphirhynchus platorhynchus) in the Missouri River. The multidisciplinary research strategy includes components of behavior, physiology, habitat use, habitat availability, and population modeling of all life stages. Shovelnose sturgeon are used to design the strategy because they are closely related to the pallid sturgeon and are often used as a surrogate species to develop new research tools or to examine the effects of management actions or environmental variables on sturgeon biology and habitat use. During fiscal years 2005 and 2006, the U.S. Army Corps of Engineers (USACE) provided funds to USGS for tasks associated with the Comprehensive Sturgeon Research Program (CSRP) and for tasks associated with evaluation of the Sturgeon Response to Flow Modifications (SRFM). Because work activities of CSRP and SRFM are so integrated, we are providing information on activities that have been consolidated at the task level. These task activities represent chapters in this report.

Open-File Report↗
USGS2007

Project overview: Chapter A in Factors affecting the reproduction, recruitment, habitat, and population dynamics of pallid sturgeon and shovelnose sturgeon in the Missouri River

For more than a hundred years, human activities have modified the natural forces that control the Missouri River and its native fish fauna. While the ecological effects of regulation and channel engineering are understood in general, the current understanding is not sufficient to guide river restoration and management. The U.S. Geological Survey (USGS) is in the third year of a multiagency research effort to determine the ecological requirements for reproduction and survival of the endangered pallid sturgeon ( Scaphirhynchus albus ) and shovelnose sturgeon ( Scaphirhynchus platorhynchus ) in the Missouri River. The multidisciplinary research strategy includes components of behavior, physiology, habitat use, habitat availability, and population modeling of all life stages. Shovelnose sturgeon are used to design the strategy because they are closely related to the pallid sturgeon and are often used as a surrogate species to develop new research tools or to examine the effects of management actions or environmental variables on sturgeon biology and habitat use. During fiscal years 2005 and 2006, the U.S. Army Corps of Engineers (USACE) provided funds to USGS for tasks associated with the Comprehensive Sturgeon Research Program (CSRP) and for tasks associated with evaluation of the Sturgeon Response to Flow Modifications (SRFM). Because work activities of CSRP and SRFM are so integrated, we are providing information on activities that have been consolidated at the task level. These task activities represent chapters in this report.

Missouri River↗
USGS2021

Sediment mobility and river corridor assessment for a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California

This river corridor assessment documents sediment mobility and river response to flood disturbance along a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California. Field and remote sensing methods were used to assess fundamental indicators of active sediment transport and river response to a combination of natural runoff events and reservoir releases during the study period from 2005 to 2019. Discharge measurements at two gaged sites and bed-material samples at two ungaged sites provided direct and indirect evidence of mobile bed conditions, scour and fill, and surface flushing of fine sediment. Available remote-sensing datasets collected in 2005, 2009, 2010, and 2016 were used to determine sediment storage, flood inundation boundaries, and provide indirect evidence of flood-induced scour. These datasets validate channel-maintenance flows defined by Shea and others (2016). During the study period, flows greater than or equal to 6,030 cubic feet per second mobilized the substrate, caused localized scour, and flushed fine sediment from bar surfaces. Flows greater than or equal to 10,400 cubic feet per second stripped vegetation from bars and floodplains and produced deeper scour. Flood disturbance within the study reach is produced by the combined effect of natural flows and reservoir releases, which resulted in mobile bed conditions during the study period. Periodic scour and substrate disturbance are considered by the U.S. Fish and Wildlife Service to be integral for managing disease-induced mortality of juvenile and adult salmonids. Substrate conditions conducive to parasites that host infectious diseases, particularly Ceratonova shasta, occur periodically. Additional studies are required to determine whether disease prevalence can be mitigated by well-timed reservoir releases. Study results are useful for interpreting linkages among physical and biological processes and for evaluating the effectiveness of flow management targeted to improve river bed conditions for endangered salmonid populations.

California↗
USGS2007

Water-quality characteristics for selected sites within the Milwaukee Metropolitan Sewerage District planning area, Wisconsin, February 2004-September 2005

The Milwaukee Metropolitan Sewerage District (MMSD) Corridor Study is a three-phase project designed to improve the understanding of water resources in the MMSD planning area to assist managers and policy makers in their decisions. Phase I of the Study involved the compilation of existing data from multiple agencies into a single database. These data were analyzed to identify spatial, temporal, and technological gaps in the planning area, and were used to develop Phase II of the Study. Phase II, the subject of this report, involved an intensive data-collection effort by the U.S. Geological Survey (USGS) in cooperation with MMSD (from February, 2004, through September, 2005). This phase addressed the data gaps identified in Phase I and completed a baseline assessment of water quality for selected stream and harbor sites in the MMSD planning area. This baseline assessment included evaluations of surface-water chemistry and microbial concentrations in the streams and harbor sites; additionally, stream sites were evaluated for discharge, sediment chemistry, fish-tissue chemistry, habitat, and the quality of biological communities (including fish, macroinvertebrates, and algae). In all, data were collected at 15 stream and 6 harbor sites within the MMSD planning area, including manual sampling and analysis for more than 220 water-quality properties and constituents at all 21 sites, stream-discharge data for 14 stream sites, and automated water-quality sampling at 4 stream sites. A bioassessment during autumn 2004 included collection of biologic-community data and stream-habitat data at wadeable streams. Quartiles of Phase II aggregate bioassessment rankings were used to divide the 14 wadeable stream sites into four groups to investigate relations between bioassessment data and site characteristic and water-quality data. Quartile numbers reflect relative water quality: quartile 1 contained sites where the bioassessment data indicated the least-degraded water quality among those sampled, and quartile 4 contained sites that indicated the most-degraded water quality. Quartiles contained the following stream sites: Quartile 1: Milwaukee River near Cedarburg, Milwaukee River at Milwaukee, Jewel Creek, and Menomonee River at Menomonee Falls; Quartile 2: Willow Creek, Root River near Franklin, and Root River at Grange Avenue; Quartile 3: Menomonee River at Wauwatosa, Oak Creek, and Little Menomonee River; and Quartile 4: Honey Creek, Underwood Creek, Lincoln Creek, and Kinnickinnic River. Site characteristics (in this case, drainage area and land use) and selected water-quality data were summarized based on the four bioassessment quartiles to determine if there were relations with the aggregate bioassessment rankings. In general, sites having the largest drainage basins with the lowest proportion of urban land use were in quartile 1, and the smallest drainage basins with the highest proportion of urban land use were in quartile 4. Major ions, indicator organisms, and wastewater compounds generally had the lowest overall results in quartile 1 and highest overall results in quartile 4, with intermediate results in quartiles 2 and 3. Results for other constituent types (nutrients, mercury, pathogenic organisms, and bed sediment) were mixed, with results for some constituents decreasing from quartile 1 to quartile 4. Where sufficient Phase I data were available, summary statistics (including medians) for chemical and biological data were calculated, allowing some comparisons to be made between Phase I and Phase II data. Comparisons between Phase I and Phase II results indicated a variety of changes with respect to water quality. Concentrations of chloride, nitrate, chlorophyll a, total phosphorus in water; arsenic in bed sediment; and fish Index of Biotic Integrity ratings generally indicated declines in water quality. However, concentrations of total nitrogen, suspended sediment, and fecal coliform in water; some trace eleme

Wisconsin↗
USGS2011

Predicting phenology by integrating ecology, evolution and climate science

Forecasting how species and ecosystems will respond to climate change has been a major aim of ecology in recent years. Much of this research has focused on phenology – the timing of life‐history events. Phenology has well‐demonstrated links to climate, from genetic to landscape scales; yet our ability to explain and predict variation in phenology across species, habitats and time remains poor. Here, we outline how merging approaches from ecology, climate science and evolutionary biology can advance research on phenological responses to climate variability. Using insight into seasonal and interannual climate variability combined with niche theory and community phylogenetics, we develop a predictive approach for species’ reponses to changing climate. Our approach predicts that species occupying higher latitudes or the early growing season should be most sensitive to climate and have the most phylogenetically conserved phenologies. We further predict that temperate species will respond to climate change by shifting in time, while tropical species will respond by shifting space, or by evolving. Although we focus here on plant phenology, our approach is broadly applicable to ecological research of plant responses to climate variability.

Global Change Biology↗
USGS2007

Relations of principal components analysis site scores to algal-biomass, habitat, basin-characteristics, nutrient, and biological-community data in the Upper Wabash River Basin, Indiana, 2003

Data were gathered from May through October 2003 at 38 randomly selected sites in the Upper Wabash River Basin, Indiana, for algal biomass, habitat, nutrients, and biological communities (fish and invertebrates). Basin characteristics (drainage area and land use) and biological-community attributes and metric scores were determined for each sampling site's basin. Yearly Principal Components Analysis site scores were calculated for algal biomass (periphyton and seston). The yearly Principal Components Analysis site scores for the first axis (PC1) were related, using Spearman's rho, to the seasonal algal-biomass, basin-characteristics, habitat, seasonal nutrient, biological-community attribute and metric score data. The periphyton PC1 site score, which was most influenced by September chlorophyll a, was not related to the five basin-characteristics, nine habitat, or 12 nutrient variables examined. Of the 43 fish-community attributes and metric scores examined, the periphyton PC1 was negatively related to one attribute (tolerant percent) and positively related to one metric score (insectivore percent metric score). Of the 43 invertebrate-community attributes and metric scores examined, the periphyton PC1 was negatively related to three attributes (Ephemeroptera, Plecoptera, and Trichoptera (EPT) count, EPT-to-total ratio, and number of taxa) and four metric scores (EPT count metric score, EPT to total ratio metric score, macroinvertebrate Index of Biotic Integrity metric score, and number of taxa metric score). The seston PC1 was not related to the five basin-characteristics, nine habitat, or 12 nutrient variables or to the 43 fish- and 21 invertebrate-community attributes or metric scores examined. To understand how the choice of sampling sites might have affected the results, an analysis of the drainage area and land use was done. The random site selection in 2003 in the Upper Wabash River Basin was skewed to small streams. The lack of large streams in the Upper Wabash River Basin could account for the few relations among the seston and the biological-community data. The values for nutrients (nitrate, total Kjeldahl nitrogen, total nitrogen, and total phosphorus) and chlorophyll a (periphyton and seston) were compared to published U.S. Environmental Protection Agency (USEPA) values for Aggregate Nutrient Ecoregions VI and VII and USEPA Level III Ecoregions 55 and 56. Several nutrient values were greater than the 25th percentile of the published USEPA values. Chlorophyll a (periphyton and seston) values either were greater than the 25th percentile of published USEPA values or extended data ranges in the Aggregate Nutrient and Level III Ecoregions. If the proposed values for the 25th percentile were adopted as nutrient water-quality criteria, many samples in the Upper Wabash River Basin would have exceeded the criteria.

Indiana↗
USGS2023

Scenario-Based Decision Analysis: Integrated scenario planning and structured decision making for resource management under climate change

Managing resources under climate change is a high-stakes and daunting task, especially because climate change and associated complex biophysical responses engender sustained directional changes as well as abrupt transformations. This environmental non-stationarity challenges assumptions and expectations among scientists, managers, rights holders, and stakeholders. These challenges are anything but straightforward – a high degree of uncertainty impedes our ability to predict the environmental trajectory with confidence, and affected resources often span multiple governance jurisdictions or are subject to competing management objectives. Fortunately, tools exist to help grapple with such challenges. Two commonly used tools are scenario planning (SP) and structured decision making (SDM). SP is a well-established approach for assessing system response and facilitating decision making under a wide range of conditions that are uncertain and uncontrollable, such as those associated with adapting to climate change. However, SP lacks a defined structure for establishing objectives, quantifying tradeoffs, and evaluating the performance of candidate decisions to meet those objectives. SDM, on the other hand, is rooted in decision theory and focuses on explicit (often quantitative) assessment of the expected outcomes of choosing among a set of decision alternatives. SDM has been criticized for an inability to account for surprises and for imposing an overly narrow framing of problems to increase tractability. We discuss the strengths and limitations of SDM and SP as experienced through their application in various resource-management contexts, and then propose a new generalized framework – Scenario-Based Decision Analysis (SBDA) – that integrates these complementary approaches. SBDA structures resource management problems and solutions while considering uncertainties and surprises to inform resource management decision making.

Biological Conservation↗
USGS2023

Genetic erosion in an endangered desert fish during a multidecadal megadrought despite long-term supportive breeding

Human water use combined with a recent megadrought have reduced river and stream flow through the Southwestern United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow. This species experiences ‘boom-and-bust’ population dynamics where large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We leveraged demographic and genetic data from wild and hatchery individuals to understand the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remains low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size (N eD ) were positively associated ( r = 0.53) with wild/total abundance, but as the proportion of hatchery-origin spawners increased, N eD was reduced ( r = -0.55). Megadrought limits wild spawner abundance and precludes refreshment of hatchery brood stocks with wild fish, hence we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.

New Mexico↗
USGS2013

Tracking animals in freshwater with electronic tags: past, present and future

Considerable technical developments over the past half century have enabled widespread application of electronic tags to the study of animals in the wild, including in freshwater environments. We review the constraints associated with freshwater telemetry and biologging and the technical developments relevant to their use. Technical constraints for tracking animals are often influenced by the characteristics of the animals being studied and the environment they inhabit. Collectively, they influence which and how technologies can be used and their relative effectiveness. Although radio telemetry has historically been the most commonly used technology in freshwater, passive integrated transponder (PIT) technology, acoustic telemetry and biologgers are becoming more popular. Most telemetry studies have focused on fish, although an increasing number have focused on other taxa, such as turtles, crustaceans and molluscs. Key technical developments for freshwater systems include: miniaturization of tags for tracking small-size life stages and species, fixed stations and coded tags for tracking large samples of animals over long distances and large temporal scales, inexpensive PIT systems that enable mass tagging to yield population- and community-level relevant sample sizes, incorporation of sensors into electronic tags, validation of tag attachment procedures with a focus on maintaining animal welfare, incorporation of different techniques (for example, genetics, stable isotopes) and peripheral technologies (for example, geographic information systems, hydroacoustics), development of novel analytical techniques, and extensive international collaboration. Innovations are still needed in tag miniaturization, data analysis and visualization, and in tracking animals over larger spatial scales (for example, pelagic areas of lakes) and in challenging environments (for example, large dynamic floodplain systems, under ice). There seems to be a particular need for adapting various global positioning system and satellite tagging approaches to freshwater. Electronic tagging provides a mechanism to collect detailed information from imperilled animals and species that have no direct economic value. Current and future advances will continue to improve our knowledge of the natural history of aquatic animals and ecological processes in freshwater ecosystems while facilitating evidence-based resource management and conservation.

Animal Biotelemetry↗