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At least 235 records · Page 13Linked to original sources
USGS2011

Proceedings of the Fourth Interagency Conference on Research in the Watersheds—Observing, Studying, and Managing for Change

These proceedings contain the abstracts, manuscripts, and posters of presentations given at the Fourth Interagency Conference on Research in the Watersheds—Observing, Studying, and Managing for Change, held at the Westmark Hotel in Fairbanks, Alaska, September 26–30, 2011. The conference was jointly hosted by the Bureau of Land Management and the National Park Service. Watersheds face resource impacts driven by accelerated change related to land use, population, and climate. About every three years a conference is held to bring together watershed researchers, observers, and managers to share scientific advances and management strategies. This year, the Fourth ICRW took a wider perspective on watershed science and examined some pressing issues of watershed science and management in our largest and perhaps most vulnerable state, Alaska. The purpose of the conference was to better understand the processes driving change and help managers incorporate societal needs and scientific uncertainty in the management of natural resources. The conference echoed similar themes to the last, highlighting the challenges of managing watersheds based on available science when considerably uncertainty remains regarding the hypothesized relationships between observed environmental changes and their ultimate effects. For example, while the scientific case for anthropogenic climate change has been well presented, confirming possible cause and effect relationships between climatic change and physical and ecological impacts in highly variable, natural systems continues to represent a scientific challenge. This goal becomes even more difficult when superimposed upon a long history of natural resource and land management practices that have fundamentally changed the physical, chemical and biological processes important in maintaining naturally functioning ecosystems. Designing and implementing studies to better understand watersheds and clearly communicating the findings to decisionmakers will be the primary challenge for natural resource scientists and managers into the foreseeable future.

Scientific Investigations Report↗
USGS2011

Advancing environmental toxicology through chemical dosimetry: External exposures versus tissue residues

The tissue residue dose concept has been used, although in a limited manner, in environmental toxicology for more than 100 y. This review outlines the history of this approach and the technical background for organic chemicals and metals. Although the toxicity of both can be explained in tissue residue terms, the relationship between external exposure concentration, body and/or tissues dose surrogates, and the effective internal dose at the sites of toxic action tends to be more complex for metals. Various issues and current limitations related to research and regulatory applications are also examined. It is clear that the tissue residue approach (TRA) should be an integral component in future efforts to enhance the generation, understanding, and utility of toxicity testing data, both in the laboratory and in the field. To accomplish these goals, several key areas need to be addressed: 1) development of a risk-based interpretive framework linking toxicology and ecology at multiple levels of biological organization and incorporating organism-based dose metrics; 2) a broadly applicable, generally accepted classification scheme for modes/mechanisms of toxic action with explicit consideration of residue information to improve both single chemical and mixture toxicity data interpretation and regulatory risk assessment; 3) toxicity testing protocols updated to ensure collection of adequate residue information, along with toxicokinetics and toxicodynamics information, based on explicitly defined toxicological models accompanied by toxicological model validation; 4) continued development of residueeffect databases is needed ensure their ongoing utility; and 5) regulatory guidance incorporating residue-based testing and interpretation approaches, essential in various jurisdictions. ??:2010 SETAC.

Integrated Environmental Assessment and Management↗
USGS2021

A food web including parasites for kelp forests of the Santa Barbara Channel, California

We built a high-resolution topological food web for the kelp forests of the Santa Barbara Channel, California, USA that includes parasites and significantly improves resolution compared to previous webs. The 1,098 nodes and 21,956 links in the web describe an economically, socially, and ecologically vital system. Nodes are broken into life-stages, with 549 free-living life-stages (492 species from 21 Phyla) and 549 parasitic life-stages (450 species from 10 Phyla). Links represent three kinds of trophic interactions, with 9,352 predator-prey links, 2,733 parasite-host links and 9,871 predator-parasite links. All decisions for including nodes and links are documented, and extensive metadata in the node list allows users to filter the node list to suit their research questions. The kelp-forest food web is more species-rich than any other published food web with parasites, and it has the largest proportion of parasites. Our food web may be used to predict how kelp forests may respond to change, will advance our understanding of parasites in ecosystems, and fosters development of theory that incorporates large networks.

California↗
USGS2009

Application of the Hydroecological Integrity Assessment Process for Missouri Streams

Natural flow regime concepts and theories have established the justification for maintaining or restoring the range of natural hydrologic variability so that physiochemical processes, native biodiversity, and the evolutionary potential of aquatic and riparian assemblages can be sustained. A synthesis of recent research advances in hydroecology, coupled with stream classification using hydroecologically relevant indices, has produced the Hydroecological Integrity Assessment Process (HIP). HIP consists of (1) a regional classification of streams into hydrologic stream types based on flow data from long-term gaging-station records for relatively unmodified streams, (2) an identification of stream-type specific indices that address 11 subcomponents of the flow regime, (3) an ability to establish environmental flow standards, (4) an evaluation of hydrologic alteration, and (5) a capacity to conduct alternative analyses. The process starts with the identification of a hydrologic baseline (reference condition) for selected locations, uses flow data from a stream-gage network, and proceeds to classify streams into hydrologic stream types. Concurrently, the analysis identifies a set of non-redundant and ecologically relevant hydrologic indices for 11 subcomponents of flow for each stream type. Furthermore, regional hydrologic models for synthesizing flow conditions across a region and the development of flow-ecology response relations for each stream type can be added to further enhance the process. The application of HIP to Missouri streams identified five stream types ((1) intermittent, (2) perennial runoff-flashy, (3) perennial runoff-moderate baseflow, (4) perennial groundwater-stable, and (5) perennial groundwater-super stable). Two Missouri-specific computer software programs were developed: (1) a Missouri Hydrologic Assessment Tool (MOHAT) which is used to establish a hydrologic baseline, provide options for setting environmental flow standards, and compare past and proposed hydrologic alterations; and (2) a Missouri Stream Classification Tool (MOSCT) designed for placing previously unclassified streams into one of the five pre-defined stream types.

Open-File Report↗
USGS2016

Predictive mapping of seabirds, pinnipeds and cetaceans off the Pacific Coast of Washington

About this report This report supports Washington-led marine spatial planning and responsible stewardship of natural and cultural resources by the Olympic Coast National Marine Sanctuary. Washington state agencies and the sanctuary continually seek the best available science to improve management of marine uses and stewardship of resources (Etheridge et al., 2010; Washington Department of Fish and Wildlife, 2015a). This report and associated data provide new, state- and sanctuary-requested information on seabird, pinniped, and cetacean distributions. Through spatial planning, information on species distributions can help to identify high-value conservation areas, minimize adverse effects of ocean uses and mitigate impacts of coastal hazards. Correspondingly, the Washington Department of Fish and Wildlife has already begun to use the maps of predicted relative density presented in this report to identify ecologically important areas off the Pacific Coast of Washington and apply this information to plan for offshore renewable energy development. This is the culmination of three years of work to compile information on seabirds, pinnipeds, and cetaceans, and advance a modeling framework that can integrate data sets and develop accurate predictions of relative density for important species off the Pacific Coast of Washington. Previous reports, which evaluated existing datasets of at-sea observations (Menza et al., 2014; Kracker and Menza, 2015) and presented superseded versions of seabird models (Menza et al., 2015), provided base information for this report. In addition to the maps in this published report, all new seabird, pinniped and cetacean predictions will be made publicly available as digital geospatial data through the National Centers for Environmental Information. This research supports the National Oceanic and Atmospheric Administration (NOAA) Coastal Zone Management Program, a voluntary partnership between the federal government and U.S. coastal and Great Lakes states and territories authorized by the Coastal Zone Management Act (CZMA) of 1972 to address national coastal issues. The act provides the basis for protecting, restoring, and responsibly developing our nation’s diverse coastal communities and resources. To meet the goals of the CZMA, the national program takes a comprehensive approach to coastal resource management – balancing the often competing and occasionally conflicting demands of coastal resource use, economic development, and conservation. A wide range of issues are addressed through the program, including coastal development, water quality, public access, habitat protection, energy facility siting, ocean governance and planning, coastal hazards, and climate change. Accurate maps of seabird and marine mammal distributions are an important tool for making informed management decisions that affect all of these issues.

Washington↗
USGS2020

Spatial conservation planning under uncertainty using modern portfolio theory and nash bargaining solution

In recent years, researchers from interdisciplinary teams involving ecologists, economists and operations re- searchers collaborated to provide decision support tools to address the challenges of preserving biodiversity by optimizing the design of reserves. The goal of this paper is to further advance this area of research and provide new solutions to solve complex Spatial Conservation Planning (SCP) problems under uncertainty that consider risk preferences of decision makers. Our approach employs modern portfolio theory to address uncertainties in SCP problems, and involves two conflicting objectives: maximizing return and minimizing risk. We apply concepts from game theory such as the Nash bargaining solution to directly compute a desirable Pareto-optimal solution for the proposed bi-objective optimization formulation in natural resource management problems. We demonstrate with numerical examples that by directly computing a Nash bar- gaining solution, a Binary Quadratically Constrained Quadratic Program (BQCQP) can be solved. We show that our approach (implementable with commercial solvers such as CPLEX) can effectively solve the proposed BQCQP for much larger problems than previous approaches published in the ecological literature. Optimal solutions for problems with less than 400 parcels can be computed within a minute. Near optimal solutions (within at most 0.2% gap from an optimal solution) for high-dimensional problems involving up to 800 parcels can be computed within 8 hours on a standard computer. We have presented a new approach to solve SCP optimization problems while considering uncertainty and risk tolerance of decision makers. Our new approach expands considerably the applicability of such SCP optimization methods to address real conservation problems.

Ecological Modelling↗
USGS2014

Movement-based estimation and visualization of space use in 3D for wildlife ecology and conservation

Advances in digital biotelemetry technologies are enabling the collection of bigger and more accurate data on the movements of free-ranging wildlife in space and time. Although many biotelemetry devices record 3D location data with x, y , and z coordinates from tracked animals, the third z coordinate is typically not integrated into studies of animal spatial use. Disregarding the vertical component may seriously limit understanding of animal habitat use and niche separation. We present novel movement-based kernel density estimators and computer visualization tools for generating and exploring 3D home ranges based on location data. We use case studies of three wildlife species – giant panda, dugong, and California condor – to demonstrate the ecological insights and conservation management benefits provided by 3D home range estimation and visualization for terrestrial, aquatic, and avian wildlife research.

PLoS ONE↗
USGS2011

Infectious diseases in Yellowstone’s canid community

Each summer Yellowstone Wolf Project staff visit den sites to monitor the success of wolf reproduction and pup rearing behavior. For the purposes of wolf monitoring, Yellowstone National Park (YNP) is divided into two study areas, the northern range and the interior, each distinguished by their ecological and physiographical differences. The 1,000 square kilometer northern range, characterized by lower elevations (1,500–2,200 m), serves as prime winter habitat for ungulates and supports a higher density of wolves than the interior (20–99 wolves/1,000 km 2 versus 2–11 wolves/1,000 km 2 ). The interior of the park encompasses 7,991 square kilometers, is higher in elevation, receives higher annual snowfall, and generally supports lower densities of wolves and ungulates. During the Yellowstone Wolf Project’s 2005 observations on the northern range, researchers noticed that some wolf pups were disappearing and those that remained were unusually listless. The Slough Creek pups, at first numbering 18, dwindled to three survivors. Similar findings were mirrored at other den sites across the northern range. When annual den surveys were conducted in late July, all that remained were scattered piles of bones and fur. Coyotes suffered similar setbacks in 2005, with many of the survivors exhibiting neurological shakes and tremors. The park’s canids had been affected by something, but what? Prompted by what seemed to be a disease outbreak, the Yellowstone Wolf Project, the Yellowstone Ecological Research Center (YERC), and the University of Minnesota decided to take several collaborative approaches toward improving our understanding of the presence and role of infectious disease in Yellowstone’s canid community. Several serological studies have been conducted in the past among the park’s coyotes (Gese et al. 1997) and cougars (Biek 2006), providing a helpful foundation on which to build and compare. A serological survey was conducted, using serum samples collected during routine wolf and coyote captures over a period of 18 years (Almberg et al. 2009). Simulation models were used to explore the dynamics of canine distemper virus (Almberg et al. 2010)—one of the more prominent pathogens in terms of its effects on its hosts—and several long-term pathogen surveillance projects were initiated which are intended to someday provide a foundation for more advanced genetic-based analyses of pathogen dynamics. Since these initial efforts, the group has also expanded the research to include a study of sarcoptic mange, which began affecting wolves and coyotes in YNP in 2006 and 2007.

Yellowstone National Park↗
USGS2022

A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush ( Artemisia tridentata ; Asteraceae), which was once the dominant shrub over 1,000,000 km 2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush ( A. tridentata subsp. tridentata ) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.

Arizona, California, Colorado, Idaho, Montana, Neb↗
USGS2023

Viewing river corridors through the lens of critical zone science

River corridors integrate the active channels, geomorphic floodplain and riparian areas, and hyporheic zone while receiving inputs from the uplands and groundwater and exchanging mass and energy with the atmosphere. Here, we trace the development of the contemporary understanding of river corridors from the perspectives of geomorphology, hydrology, ecology, and biogeochemistry. We then summarize contemporary models of the river corridor along multiple axes including dimensions of space and time, disturbance regimes, connectivity, hydrochemical exchange flows, and legacy effects of humans. We explore how river corridor science can be advanced with a critical zone framework by moving beyond a primary focus on discharge-based controls toward multi-factor models that identify dominant processes and thresholds that make predictions that serve society. We then identify opportunities to investigate relationships between large-scale spatial gradients and local-scale processes, embrace that riverine processes are temporally variable and interacting, acknowledge that river corridor processes and services do not respect disciplinary boundaries and increasingly need integrated multidisciplinary investigations, and explicitly integrate humans and their management actions as part of the river corridor. We intend our review to stimulate cross-disciplinary research while recognizing that river corridors occupy a unique position on the Earth's surface.

Frontiers in Water↗
USGS2013

A computer model to forecast wetland vegetation changes resulting from restoration and protection in coastal Louisiana

The coastal wetlands of Louisiana are a unique ecosystem that supports a diversity of wildlife as well as a diverse community of commercial interests of both local and national importance. The state of Louisiana has established a 5-year cycle of scientific investigation to provide up-to-date information to guide future legislation and regulation aimed at preserving this critical ecosystem. Here we report on a model that projects changes in plant community distribution and composition in response to environmental conditions. This model is linked to a suite of other models and requires input from those that simulate the hydrology and morphology of coastal Louisiana. Collectively, these models are used to assess how alternative management plans may affect the wetland ecosystem through explicit spatial modeling of the physical and biological processes affected by proposed modifications to the ecosystem. We have also taken the opportunity to advance the state-of-the-art in wetland plant community modeling by using a model that is more species-based in its description of plant communities instead of one based on aggregated community types such as brackish marsh and saline marsh. The resulting model provides an increased level of ecological detail about how wetland communities are expected to respond. In addition, the output from this model provides critical inputs for estimating the effects of management on higher trophic level species though a more complete description of the shifts in habitat.

Louisiana↗
USGS2011

Rapid diagnosis of avian influenza virus in wild birds: Use of a portable rRT-PCR and freeze-dried reagents in the field

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAI) of the H5N1 subtype, prompting surveillance along migratory flyways. Sampling of wild birds for avian influenza virus (AIV) is often conducted in remote regions, but results are often delayed because of the need to transport samples to a laboratory equipped for molecular testing. Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is a molecular technique that offers one of the most accurate and sensitive methods for diagnosis of AIV. The previously strict lab protocols needed for rRT-PCR are now being adapted for the field. Development of freeze-dried (lyophilized) reagents that do not require cold chain, with sensitivity at the level of wet reagents has brought on-site remote testing to a practical goal. Here we present a method for the rapid diagnosis of AIV in wild birds using an rRT-PCR unit (Ruggedized Advanced Pathogen Identification Device or RAPID, Idaho Technologies, Salt Lake City, UT) that employs lyophilized reagents (Influenza A Target 1 Taqman; ASAY-ASY-0109, Idaho Technologies). The reagents contain all of the necessary components for testing at appropriate concentrations in a single tube: primers, probes, enzymes, buffers and internal positive controls, eliminating errors associated with improper storage or handling of wet reagents. The portable unit performs a screen for Influenza A by targeting the matrix gene and yields results in 2-3 hours. Genetic subtyping is also possible with H5 and H7 primer sets that target the hemagglutinin gene. The system is suitable for use on cloacal and oropharyngeal samples collected from wild birds, as demonstrated here on the migratory shorebird species, the western sandpiper (Calidrus mauri) captured in Northern California. Animal handling followed protocols approved by the Animal Care and Use Committee of the U.S. Geological Survey Western Ecological Research Center and permits of the U.S. Geological Survey Bird Banding Laboratory. The primary advantage of this technique is to expedite diagnosis of wild birds, increasing the chances of containing an outbreak in a remote location. On-site diagnosis would also prove useful for identifying and studying infected individuals in wild populations. The opportunity to collect information on host biology (immunological and physiological response to infection) and spatial ecology (migratory performance of infected birds) will provide insights into the extent to which wild birds can act as vectors for AIV over long distances.

Journal of Visualized Experiments↗
USGS2025

Are behavioural ecotoxicity endpoints relevant at the population level? Evidence-based insights for environmental protection

A substantial body of evidence exists demonstrating that exposure to environmental contaminants can alter animal behavior. Moreover, methodological and technological advancements, as well as increasing standardization, mean that behavioral ecotoxicity studies are more rigorous and reliable than ever before. Despite this, behavioral data are still seldom used in the risk assessment and regulation of chemicals. This is partly due to a lack of clarity among some stakeholders about whether changes in behavior at the individual level result in population-level outcomes. To address this, we first consider the state of evidence within the field of behavioral ecotoxicology linking individual-level behavioral alterations with population-level consequences. We then assess the evidence from behavioral ecology and other neighboring fields that supports this link. Further, we evaluate whether some behavioral endpoints are more easily tied to population-level changes than others. In this regard, we propose combining insights from two complementary ecological frameworks─the functional trait framework and the limiting traits framework─to evaluate which behaviors should be prioritized in ecotoxicological research and regulatory efforts. We contend that the link between behavioral changes and population-level outcomes is evident, with behavioral endpoints representing a highly valuable yet so far underutilized line of evidence in applied environmental protection.

Environmental Science and Technology↗
USGS2022

Democratizing macroecology: Integrating unoccupied aerial systems with the National Ecological Observatory Network

Macroecology research seeks to understand ecological phenomena with causes and consequences that accumulate, interact, and emerge across scales spanning several orders of magnitude. Broad-extent, fine-grain information (i.e., high spatial resolution data over large areas) is needed to adequately capture these cross-scale phenomena, but these data have historically been costly to acquire and process. Unoccupied aerial systems (UAS or drones carrying a sensor payload) and the National Ecological Observatory Network (NEON) make the broad-extent, fine-grain observational domain more accessible to researchers by lowering costs and reducing the need for highly specialized equipment. Integration of these tools can further democratize macroecological research, as their strengths and weaknesses are complementary. However, using these tools for macroecology can be challenging because mental models are lacking, thus requiring large up-front investments in time, energy, and creativity to become proficient. This challenge inspired a working group of UAS-using academic ecologists, NEON professionals, imaging scientists, remote sensing specialists, and aeronautical engineers at the 2019 NEON Science Summit in Boulder, Colorado, to synthesize current knowledge on how to use UAS with NEON in a mental model for an intended audience of ecologists new to these tools. Specifically, we provide (1) a collection of core principles for collecting high-quality UAS data for NEON integration and (2) a case study illustrating a sample workflow for processing UAS data into meaningful ecological information and integrating it with NEON data collected on the ground—with the Terrestrial Observation System—and remotely—from the Airborne Observation Platform. With this mental model, we advance the democratization of macroecology by making a key observational domain—the broad-extent, fine-grain domain—more accessible via NEON/UAS integration.

Ecosphere↗
USGS2009

IPANE: Could New England's Early Detection Network benefit eastern Canada?

The Invasive Plant Analysis of New England (IPANE: ipane.org) is a multifaceted approach to regional early detection of invasive plants. IPANE, was founded in 2001 to create a comprehensive six state New England regional partnership to: minimize the ecological damage caused by invasive plants; provide reliable and accessible educational material; maintain a network of professional and trained volunteers to gather information and to locate new incursions; provide a web-accessible database and maps of invasive and potentially invasive plants; conduct and encourage research on the biology and ecology of invasive plants; and, use program-generated data to develop predictive distribution models for the region. This program uses the synergy of all the components to create a regional early detection and rapid assessment network to curtail new invasions before they become widespread on the regional landscape. IPANE is a model for the United States Geological Survey National Early Detection Network Toolbox, a compendium of information developed for use by Network partners. In addition, an Early Detection Alert system has been developed to inform key federal and state agency staff, conservation organizations, and those with vegetation management responsibilities about new or potential invaders to the region. These include current and anticipated distribution, diagnostic characters, images, pertinent biological and control information, and key contacts. Most of the non-native species currently considered invasive by IPANE appear to be spreading into New England from the south or west. IPANE is strategically placed to act as an advanced warning system for the 5 provinces of Eastern and Maritime Canada. At the meeting held in Nova Scotia in September 2007, this idea was suggested to attendees from 4 of these 5 provinces and the Canadian government. By expanding its alert systems, IPANE could serve as a focal point for Early Detection information moving in any direction and tie Eastern Canada into the National Early Detection Network of the United States.

Conference Paper↗
USGS2024

Empirical assessments of the type and strength of stream fish habitat associations can advance understanding of functional diversity and promote effective conservation.

The ability to accurately quantify biodiversity is fundamental to understanding ecological trends, identifying drivers of declines, and selecting effective conservation options. Scientists and resource managers have grappled with what metrics best show relevant biodiversity patterns and are still practical enough to aid on-the-ground resource conservation. Our purpose is to construct empirically derived, functional habitat guilds for prairie stream fish, then recommend future directions for constructing and using diversity metrics that aid field-based conservation. Working in the Upper Neosho River, KS, USA, we used univariate methods, cluster analysis, non-metric multi-dimensional scaling, and an analysis of similarity to functionally group stream fish taxa. The 11 most abundant fish species grouped into seven ecological guilds: riffle specialist, pool specialist, riffle generalist, pool generalist, riffle–run generalist, pool–run generalist, and generalist. Combining the habitat type and strength of association added ecological accuracy to our species groups. Employing multiple statistical methods increased confidence and generality in our grouping results. Moving forward will require a coordinated, coalition-driven, conservation-related strategy on which researchers and practitioners collaborate to synthesize diverse empirical results, organize general principles of structure and function, and balance accuracy with practicality.

Kansas↗
USGS2017

2010-2015 Juvenile fish ecology in the Nisqually River Delta and Nisqually Reach Aquatic Reserve

The return of tidal inundation to over 750 acres of the U. S. Fish and Wildlife Service Billy Frank Jr. Nisqually National Wildlife Refuge (NNWR) in fall of 2009 was the crowning moment in the effort to protect and restore the Nisqually Delta. The Nisqually NWR project complemented three earlier restoration projects completed by the Nisqually Indian Tribe (Tribe) on tribal property to restore over 900 acres of the estuary, representing the largest estuary restoration project in the Pacific Northwest and one of the most significant advances to date towards the recovery of Puget Sound (USFWS 2005). In 2011 the Washington Department of Natural Resources (WADNR established the over 14000 acre Nisqually Reach Aquatic Reserve (Reserve), complementing the protection and restoration successes in the Nisqually Delta. The Reserve includes all state-owned aquatic lands around Anderson, Ketron and Eagle islands and part of McNeil Island (Figure 1, WDNR 2011). The Reserve also includes a diverse assemblage of nearshore and offshore habitats important to resident and migratory fish including federal endangered species act listed fish like Chinook salmon (Oncorynchus tshawytscha) and steelhead (O. mykiss). Studies in the Nisqually Estuary (Ellings and Hodgson 2007, David et al. 2014, Ellings et al. 2016) and South Puget Sound (Duffy 2003) have summarized fish use of the area. However, the fish ecology of the reserve had not been systematically surveyed. The Tribe, U.S. Geological Survey (USGS), NNWR, Nisqually River Foundation (NRF), and others are currently conducting a multi-year, interdisciplinary, hypothesis-based research and monitoring study investigating the impact of delta restoration on estuarine processes, habitat structures, and functions. Our interdisciplinary monitoring framework enables us to link key estuarine processes with habitat development and biological response at multiple scales across the restored footprint, reference marshes, and throughout the Nisqually Reach. Key research components include hydrology and sediment regime, channel and marsh topography and development, vegetation colonization, and invertebrate, bird, and fish abundance, habitat use, and foraging ecology. After the Reserve was established, the WDNR and the research partnership led by the Tribe expanded the existing delta fish ecology assessment to include sampling stations throughout the Reserve. The results of the Reserve fish ecology assessment provide a unique regional analysis of fish ecology from the Nisqually River to McNeil Island.

Salmon Recovery Program Technical Report↗
USGS2010

Assessing macroinvertebrate biodiversity in freshwater ecosystems: Advances and challenges in dna-based approaches

Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics. ?? 2010 by The University of Chicago Press.

The Quarterly Review of Biology↗