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USGS2021

Heed the data gap: Guidelines for using incomplete datasets in annual stream temperature analyses

Stream temperature data are useful for deciphering watershed processes important for aquatic ecosystems. Accurately extracting signal trends from stream temperature is essential for predicting responses of environmental and ecological indicators to change. Missing data periods are common for various reasons, and pose a challenge for scientists using temperature signal analysis to support stream research and ecological management objectives. However, the sensitivity of estimated temperature signal patterns to missing data has not been thoroughly evaluated, despite the potentially large impact on interpretation. In this study, we explored the effects of simulated missing daily data on the characterization of annual water temperature signals measured at headwater sites in the Pacific Northwest and Mid-Atlantic regions of the USA. For each site, we used linear regressions of sine-waves fitted to complete (365-d) and partial (7–357 consecutive missing data points) annual datasets of daily mean water temperature and computed three thermal parameters (mean, phase, and amplitude), which together can indicate thermally and ecologically influential watershed processes (e.g., depth and magnitude of groundwater discharge). Expected values (derived from complete datasets) ranged from 7.0 to 12.6 °C, 205 to 254 d, and 1.9 to 9.5 °C for annual mean, phase, and amplitude, respectively. While annual phase and amplitude could be accurately estimated (i.e., within 95–99% confidence intervals of expected values) with up to approximately two months of consecutively missing data, annual mean temperature required more complete datasets. We found that datasets with less than seven weeks of consecutively missing data enabled estimation of all annual signal parameters with reasonable accuracy (>75% probability of being within the 95–99% confidence intervals of expected values). Imputation of missing data expanded this range to approximately 20 weeks, with the greatest improvements in parameter estimation between 9 and 27 weeks of imputed missing data. However, caution should be exercised when applying this technique. For example, imputation improved the accuracy of parameter estimation for most sites, but accuracy decreased for some sites exhibiting strong groundwater influence. The timing of consecutive missing data points within a year had inconsistent effects on annual thermal parameter estimates among regions, years, and individual parameters. Utilizing sites with more than approximately seven consecutive weeks of missing data or 20 weeks of imputed data increases the probability of mischaracterization of annual stream thermal regimes. Understanding this limitation is vital for identifying the potential of streams to serve as climate refugia for ecological indicator species and effective future management of stream systems.

Ecological Indicators↗

USGS2012

Population dynamics of Corbicula fluminea (Müller, 1774) in mesohaline and oligohaline habitats: Invasion success in a Southern Europe estuary

Due to its range expansion and potential ecological effects, Corbicula fluminea is considered one of the most important non-indigenous species (NIS) in aquatic ecosystems. Its presence since 2003 in the upstream area of Mondego estuary (oligohaline and mesohaline sectors) was studied during thirteen months, from December 2007 to December 2008. Monthly mean abundance and biomass ranged from 542 to 11142 individuals m -2 and 13.1–20.4 g Ash Free Dry Weight m -2 , respectively. Populations of C.fluminea were composed mostly of juveniles, always present in extremely high densities compared to other estuarine ecosystems (e.g. Minho estuary) suggesting a continuous recruitment pattern. The hydraulic regime of the River Mondego favours the downstream colonization of the upper Mondego estuary by recruits produced upstream. However, salinity in these sectors of the estuary apparently neither favours growth nor the establishment of structured populations of this species. Other factors like contaminants and predation, which were not studied, could also contribute to the community structure observed.

Estuarine, Coastal and Shelf Science↗

USGS2002

A terrain-based paired-site sampling design to assess biodiversity losses from eastern hemlock decline

Biodiversity surveys are often hampered by the inability to control extraneous sources of variability introduced into comparisons of populations across a heterogenous landscape. If not specifically accounted for a priori, this noise can weaken comparisons between sites, and can make it difficult to draw inferences about specific ecological processes. We developed a terrain-based, paired-site sampling design to analyze differences in aquatic biodiversity between streams draining eastern hemlock (Tsuga canadensis) forests, and those draining mixed hardwood forests in Delaware Water Gap National Recreation Area (USA). The goal of this design was to minimize variance due to terrain influences on stream communities, while representing the range of hemlock dominated stream environments present in the park. We used geographic information systems (GIS) and cluster analysis to define and partition hemlock dominated streams into terrain types based on topographic variables and stream order. We computed similarity of forest stands within terrain types and used this information to pair hemlock-dominated streams with hardwood counterparts prior to sampling. We evaluated the effectiveness of the design through power analysis and found that power to detect differences in aquatic invertebrate taxa richness was highest when sites were paired and terrain type was included as a factor in the analysis. Precision of the estimated difference in mean richness was nearly doubled using the terrain-based, paired site design in comparison to other evaluated designs. Use of this method allowed us to sample stream communities representative of park-wide forest conditions while effectively controlling for landscape variability.

Environmental Monitoring and Assessment↗

USGS2000

Relationship of Eastern hemlock ( Tsuga canadensis ) to the ecology of small streams in Delaware Water Gap National Recreation Area

Hemlock ravines in Delaware Water Gap National Recreation Area (DEWA) are highly valued because of their distinctive aesthetic, recreational and ecological qualities. We conducted a comparative study designed to determine the potential long-term consequences to aquatic communities of the suspected transition from hemlock-dominated forests to mixed hardwood forests as a result of hemlock woolly adelgid (HWA; Adelges tsugae) induced mortality. A landscape analysis of DEWA using Geographic Information Systems (GIs) was used to select 14 hemlock and hardwood site-pairs that were similar in topography (i.e., slope, terrain shape, aspect, light levels) and stream size (first or second order) but differed in forest composition. This paired watershed approach provided a powerful means to discern the influence of hemlock forests on stream communities. This study was designed to provide an aquatic perspective on potential losses of biological diversity should hemlock forests die.

New Jersey;Pennsylvania↗

USGS2002

A reservoir landscape for age-0 largemouth bass

Landscape ecology is concerned with how ecological processes are affected by spatial patterns. Identification of heterogeneity in littoral zones has expanded the conceptual framework of aquatic landscapes. Long-term study of a reservoir largemouth bass population indicated that the amount and arrangement of habitat regulated the population processes. The distribution of age-0 largemouth bass was quantified in relation to littoral habitat and relations between landscape features and population parameters on scales from embayment to microhabitat were determined. At the embayment scale, shoreline slope and amount of gravel substratum predicted fivefold variability in abundance among four reservoir embayments. Within an embayment, these habitat features explained between 37 and 88 percent of variation in shoreline distribution of age-0 largemouth bass. At the microhabitat scale, age-0 largemouth bass exhibited patchy distributions in relation to gravel substratum at 40 percent of sites. These results indicate that the landscape scale domain for young largemouth bass is large; whereas, specific patterns explained processes across multiple scales. Distributions of age-0 largemouth bass in relation to habitat, however, were apparent on a fine scale (10 m) and these data, coupled with limited movement behavior of young largemouth bass, indicate that the ecological neighborhood of this life stage is small. Our data also suggested that some habitats may be source habitats because embayments with hypothesized higher source/sink ratios were more productive. Although patch arrangement critical to young largemouth bass ecology was not quantified, it was apparent that embayments with more complex habitats likely provided the extent of the landscape for age-0 largemouth bass in Jordan Lake. Identification of scale of patchiness (of fish distributions and habitats) for this life stage will assist in making inferences regarding complex ecological processes that can affect year-class productivity on multiple scales. ?? 2002 by the American Fisheries Society.

American Fisheries Society Symposium↗

USGS2020

Understanding and documenting the scientific basis of selenium ecological protection in support of site-specific guidelines development for Lake Koocanusa, Montana, U.S.A., and British Columbia, Canada

Modeling of ecosystems is a part of the U.S. Environmental Protection Agency’s protocol for developing site-specific selenium guidelines for protection of aquatic life. Selenium as an environmental contaminant is known to bioaccumulate and cause reproductive effects in fish and wildlife. Here we apply a modeling methodology—ecosystem-scale selenium modeling—to understand and document the scientific basis for predicting and validating ecological protection for Lake Koocanusa, a transboundary reservoir between Montana and British Columbia. A comprehensive set of site-specific data compiled from public databases (Federal, State, and Provincial) and reports by Teck Coal Ltd., is available in a companion U.S. Geological Survey data release. The tissue guideline used within modeling here to assess protection is the U.S. Environmental Protection Agency’s national selenium guideline for whole-body fish (dry weight); however, other numeric values for a whole-body guideline or other tissue types may be assumed if applicable tissue-to-tissue conversion factors are available. We consider the report assembled here as a working document that presents a model that can effectively address and structure the needs of (1) scientific understanding in representing the lake’s ecosystem and selenium biodynamics and (2) policy and management development during a decision-making process, but it is open to modification and updating as more ecologically detailed data become available. The approach brings together the main concerns involved in selenium toxicity: likelihood of high exposure, inherent species sensitivity, and close connectivity of ecosystem characteristics and behavioral ecology of predators. Detailed site-specific modeling equations are provided to document the linked factors that determine the responses of ecosystems to selenium. A series of scenarios quantifies the implications of choices of site-specific variables including food-web species, bioavailability of particulate material, and partitioning between the dissolved and particulate phases at the base of food webs. A gradient mapping tool applied to Lake Koocanusa provides a precedent for ecosystem-scale modeling of lakes by recognizing the importance of lake strata and hydrodynamics as components of modeling. Data requirements for ecosystem modeling, including ecological and hydrological process information fundamental to the dietary biodynamics of selenium in site-specific food webs, were assessed as a precursor to model validation for Lake Koocanusa. Understanding these relationships is necessary to connect modeling outcomes to reproductive effects and establish boundaries, in the case of Lake Koocanusa, for the influences of dam operation, fish-community viability, and its Clean Water Act impaired 303(d)-listing status on ecosystem function. We find that an assemblage of conditions affects the representation of Lake Koocanusa’s ecosystem within modeling scenarios but that the constructed gradient maps, mechanistic model, and associated bioaccumulation potentials portray and quantify the variables that are determinative to protection of predator species. Ecological and hydrological sorting of compiled individual data points on a site- and species-specific basis helps identify and address model uncertainties. Sources of uncertainty include (1) the scarcity of data for some environmental media compartments across time and locations, (2) the complexity of hydrodynamic conditions that can lead to seasonal ecological disconnects such as in selenium partitioning from water into particulates, and (3) the functional status of Lake Koocanusa’s ecosystem because of cumulative effects of various environmental stresses (for example, fish-community changes, flow regime changes, parasites, gonadal dysfunction, and increasing mining input-selenium concentrations since 1984). To this last point, it is important to determine where Lake Koocanusa is in an impairment-restoration cycle so as not to base protection on survivor bias, the maintenance of a currently degraded ecosystem, or normalized toxicity. In a broader context, one of the overall consequences of revised selenium regulations is that their derivation is now dependent on being able to define and understand the status of the ecosystem on which protection is based.

Montana, British Columbia↗

USGS2013

Fall diel diet composition of American eel (Anguilla rostrata) in a tributary of the Hudson River, New York, USA

American eel (Anguilla rostrata), a once common species, is now in decline throughout much of its native range in North America. There is little information on the role of American eel in river food webs. A better understanding of the diet and ecological role of American eel will help in the conservation of this important species. During autumn 2009, eel and aquatic invertebrate samples were collected from Hannacroix Creek, a tributary of the Hudson River, in Albany and Greene counties, New York, USA. Eel diet was analyzed by the eel size and time period (day or night). A high proportion of eel stomachs were empty (73%). Eel diets varied among size classes and day and night feeding periods (p = 0.001). Diet overlap was significant between small and medium eels caught both during the day (α = 0.71) and at night (α = 0.84). Nocturnal diet and nocturnal invertebrate samples were similar (α = 0.65), indicating a preference for bottom feeding during the night. Mayfly nymphs were the major prey consumed in each period by all size classes. Among eels that fed, night-feeding eels had the greatest stomach weight (as a percent of total body weight). The swim-bladder parasite, Anguillicoloides crassus, was also observed in eels of all size classes with nearly 50% afflicted.

New York↗

USGS2025

The story of the Penobscot River Ecology Mural: A 10-step process for scientists to create public art

Rivers are home to a wide variety of biota, including fishes, amphibians, reptiles, birds, freshwater mussels, aquatic insects, and microscopic organisms that fill unique niches to support broader ecosystem functions. While the general public may be aware of recreationally relevant biological life (e.g., fishes and insects to model flyfishing flies from), they may not be aware of more obscure yet important taxa. For example, freshwater mussels (Unionidae) improve water quality and clarity of rivers through filtration ( Vaughn, 2018), which is vital to riverine ecosystems. Despite this importance, lack of public knowledge about freshwater mussels is the second biggest challenge to their management ( Bouska et al., 2018). How do we best get the public to see value in underappreciated taxa to support their conservation? Public art installations can spread awareness about science effectively because they distill information for broader audiences, are eye-catching, and reach people through an emotional, aesthetic, and personal lens ( Thompson et al., 2023). While invertebrates are generally viewed by the public with fear and aversion ( Kellert, 1993) this can be ameliorated through interaction and learning, particularly for children ( Miller et al., 2025). Through cross-disciplinary collaboration between artists, scientists and the local community, we created the “Penobscot River Ecology Mural,” a scientifically informed artwork featuring underappreciated taxa like mussels and insects. In this article, we will elucidate the story of how we successfully made this piece through 10 steps, which provide a blueprint for future endeavors.

Maine↗

USGS2022

Resisting-accepting-directing: Ecosystem management guided by an ecological resilience assessment

As anthropogenic influences push ecosystems past tipping points and into new regimes, complex management decisions are complicated by rapid ecosystem changes that may be difficult to reverse. For managers who grapple with how to manage ecosystems under novel conditions and heightened uncertainty, advancing our understanding of regime shifts is paramount. As part of an ecological resilience assessment, researchers and managers have collaborated to identify alternate regimes and build an understanding of the thresholds and factors that govern regime shifts in the Upper Mississippi River System. To describe the management implications of our assessment, we integrate our findings with a recently developed framework that explicitly acknowledges ecosystem regime change and outlines management approaches of resisting change, accepting change, or directing change. More specifically, we developed guidance for using knowledge of desirability of current conditions, distance to thresholds, and general resilience (that is, an ecosystem’s capacity to cope with uncertain disturbances) to navigate the resist-accept-direct (RAD) framework. We applied this guidance to outline strategies that resist, accept, or direct change in the context of management of aquatic vegetation, floodplain vegetation, and fish communities across nearly 2000 river kilometers. We provide a case study for how knowledge of ecological dynamics can aid in assessing which management approach(es) are likely to be most ecologically feasible in a changing world. Continued learning from management decisions will be critical to advance our understanding of how ecosystems respond and inform the management of ecosystems for desirable and resilient outcomes.

Illinois, Iowa, Kentucky, Minnesota, Missouri, Wis↗

USGS2024

Implementation of controlled floods for sediment management on the Colorado River in Grand Canyon under aridification

In addition to supplying water for agriculture, cities, and industry, the Colorado River traverses the Colorado Plateau, including several of the most unique and valued National Parks and Recreation Areas in the United States. Although the water needs of these landscapes were not considered at the time water allocations were first negotiated, these needs were recognized in subsequent legislation and policy. Management goals address a range of aquatic and riparian resources, including fine sediment (sand, silt, and clay) which, in Grand Canyon, is important for ecological, cultural, and recreational resources. Over ~30 years, stakeholders, resource managers, and scientists collectively developed operational strategies for sediment management to meet goals outlined by an adaptive management program. However, prolonged drought, or “aridification,” resulting in declining runoff and the lowest reservoir storage elevations in decades has challenged those strategies. The paradigm for sustainable sediment management relies on (1) sand accumulation on the bed of the Colorado River during periods of sediment-rich tributary floods from summer/fall thunderstorms, and (2) dam-released controlled (artificial) floods, referred to as High-Flow Experiments (HFEs), to redistribute the accumulated sand to rebuild eroded bar and floodplain deposits. The management protocol, which specifies narrowly defined sand accumulation periods and HFE implementation windows, is based on implementing HFEs in late fall during the period of greatest sediment enrichment, before higher winter releases for hydropower erode the accumulated sand from the riverbed. Low dam releases associated with drought, however, have changed the pattern of sand accumulation and low reservoir elevations have prevented HFE implementation in the defined window. An alternative strategy for HFE planning and implementation was tested opportunistically in April 2023 following lower-than-normal winter dam releases. We present findings from this HFE indicating that sand enrichment and sandbar building equaled or exceeded that of HFEs conducted under the established management protocol. These findings show that management goals for sediment under conditions of prolonged drought may be achievable but will likely require substantial changes in dam management strategies.

Arizona↗

USGS2006

Ecological thresholds: The key to successful enviromental management or an important concept with no practical application?

An ecological threshold is the point at which there is an abrupt change in an ecosystem quality, property or phenomenon, or where small changes in an environmental driver produce large responses in the ecosystem. Analysis of thresholds is complicated by nonlinear dynamics and by multiple factor controls that operate at diverse spatial and temporal scales. These complexities have challenged the use and utility of threshold concepts in environmental management despite great concern about preventing dramatic state changes in valued ecosystems, the need for determining critical pollutant loads and the ubiquity of other threshold-based environmental problems. In this paper we define the scope of the thresholds concept in ecological science and discuss methods for identifying and investigating thresholds using a variety of examples from terrestrial and aquatic environments, at ecosystem, landscape and regional scales. We end with a discussion of key research needs in this area.

Ecosystems↗

USGS2011

Ecosystem approach to inland fisheries: Research needs and implementation strategies

Inland fisheries are a vital component in the livelihoods and food security of people throughout the world, as well as contributing huge recreational and economic benefits. These valuable assets are jeopardized by lack of research-based understanding of the impacts of fisheries on inland ecosystems, and similarly the impact of human activities associated with inland waters on fisheries and aquatic biodiversity. To explore this topic, an international workshop was organized in order to examine strategies to incorporate fisheries into ecosystem approaches for management of inland waters. To achieve this goal, a new research agenda is needed that focuses on: quantifying the ecosystem services provided by fresh waters; quantifying the economic, social and nutritional benefits of inland fisheries; improving assessments designed to evaluate fisheries exploitation potential; and examining feedbacks between fisheries, ecosystem productivity and aquatic biodiversity. Accomplishing these objectives will require merging natural and social science approaches to address coupled social-ecological system dynamics. ?? 2010 The Royal Society.

Conference Paper↗

USGS2017

Selenium

Selenium (Se) was discovered in 1817 in pyrite from copper mines in Sweden. It is a trace element in Earth’s crust, with an abundance of three to seven orders of magnitude less than the major rock-forming elements. Commercial use of selenium began in the United States in 1910, when it was used as a pigment for paints, ceramic glazes, and red glass. Since that time, it has had many other economic uses—notably, in the 1930s and 1940s, when it was used in rectifiers (which change alternating current to direct current), and in the 1960s, when it began to be used in the liner of photocopier drums. In the 21st century, other compounds have replaced selenium in these older products; modern uses for selenium include energy-efficient windows that limit heat transfer and thin-film photovoltaic cells that convert solar energy into electricity. In Earth’s crust, selenium is found as selenide minerals, selenate and selenite salts, and as substitution for sulfur in sulfide minerals. It is the sulfide minerals, most commonly those in porphyry copper deposits, that provide the bulk of the selenium produced for the international commodity market. Selenium is obtained as a byproduct of copper refining and recovered from the anode slimes generated in electrolytic production of copper. Because of this, the countries that have the largest resources and (or) reserves of copper also have the largest resources and (or) reserves of selenium. Because selenium occurs naturally in Earth’s crust, its presence in air, water, and soil results from both geologic reactions and human activity. Selenium is found concentrated naturally in soils that overlie bedrock with high selenium concentrations. Selenium mining, processing, use in industrial and agricultural applications, and disposal may all contribute selenium to the environment. A well-known case of selenium contamination from agricultural practices was discovered in 1983 in the Kesterson National Wildlife Refuge in California. There, waters draining from agricultural fields created wetlands with high concentrations of dissolved selenium in the water. The selenium was taken up by aquatic wildlife and caused massive numbers of embryonic deformities and deaths. Regulatory agencies have since worked to safeguard ecological and human health by creating environmental exposure guidelines based upon selenium concentrations in water and in fish tissue. Any attempt to regulate selenium concentrations requires a delicate balance because selenium occurs naturally and is also a vital nutrient for the health of wildlife, domestic stock, and humans. Selenium is commonly added as a vitamin to animal feed, and in some regions of the United States and the world, it is added as an amendment to soils for uptake by agricultural crops. The important role of selenium in economic products, energy supply, agriculture, and health will continue for well into the future. The challenge to society is to balance the benefits of selenium use with the environmental consequences of its extraction. Increased understanding of the elemental cycle of selenium in the earth may lead to new (or unconventional) sources of selenium, the discovery of new methods of extraction, and new technologies for minimizing the transfer of selenium from rock to biota, so to protect environmental and human health.

Professional Paper↗

USGS1999

Characterizing fish community diversity across Virginia landscapes: Prerequisite for conservation

The number of community types occurring within landscapes is an important, but often unprotected, component of biological diversity. Generally applicable protocols for characterizing community diversity need to be developed to facilitate conservation. We used several multivariate techniques to analyze geographic variation in the composition of fish communities in Virginia streams. We examined relationships between community composition and six landscape variables: drainage basin, physiography, stream order, elevation, channel slope, and map coordinates. We compared patterns at two scales (statewide and subdrainage-specific) to assess sensitivity of community classification to spatial scale. We also compared patterns based on characterizing communities by species composition vs. ecological composition. All landscape variables explained significant proportions of the variance in community composition. Statewide, they explained 32% of the variance in species composition and 48% of the variance in ecological composition. Typical communities in each drainage or physiography were statistically distinctive. Communities in different combinations of drainage, physiography, and stream size were even more distinctive, but composition was strongly spatially autocorrelated. Ecological similarity and species similarity of community pairs were strongly related, but replacement by ecologically similar species was common among drainage–physiography combinations. Landscape variables explained significant proportions of variance in community composition within selected subdrainages, but proportions were less than at the statewide scale, and the explanatory power of individual variables varied considerably among subdrainages. Community variation within subdrainages appeared to be much more closely related to environmental variation than to replacement among ecologically similar species. Our results suggest that taxonomic and ecological characterizations of community composition are complementary; both are useful in a conservation context. Landscape features such as drainage, physiography, and water body size generally may provide a basis for assessing aquatic community diversity, especially in regions where the biota is poorly known. Systematic conservation of community types would be a major advance relative to most current conservation programs, which typically focus narrowly on populations of imperiled species. More effective conservation of aquatic biodiversity will require new approaches that recognize the value of both species and assemblages, and that emphasize protection of key landscape-scale processes.

Ecological Applications↗

USGS2024

The state of the science and practice of stream restoration in the Chesapeake: Lessons learned to inform better implementation, assessment and outcomes

The Chesapeake Bay Program’s (CBP) Science and Technical Advisory Committee (STAC) organized and led a workshop on the science and practice of stream restoration in order to summarize the state of knowledge in order to identify ways to improve stream restoration outcomes. The workshop identified a general framework for explaining the main factors leading to stream restoration outcomes: stream degradation has occurred, leading to regulatory and policy motivations that prioritize project goals, which leads to restoration approaches, assessment and monitoring efforts, and ultimately stream restoration outcomes. In the Chesapeake Bay watershed, stream restoration often occurs in response to Clean Water Act (CWA) mandates to reduce nitrogen, phosphorus, and sediment loads to the Bay. Reviews of stream restoration outcomes summarized at the workshop showed that, in general, stream restorations have led to minimal improvement to stream aquatic biota, effective ‘stabilization’ of channel form over time, moderate improvements to water quality, and short-term negative impacts to riparian vegetation. The fundamental finding of the workshop was that often the primary goal of stream restoration projects is to improve geomorphic stability in the restored reach and downstream water quality, and not to improve local ecological conditions through ‘uplift’ (improvement of one or more ecosystem functions through a restorative activity; a term defined in Appendix D), and therefore these projects often do not improve aquatic macroinvertebrate or fish communities. This conflict in goals is a shortcoming of the currently most common regulatory driver for stream restoration (reducing downstream loads of N, P, and sediment) that could be addressed directly through diversifying goals to include biotic uplift, as biological benefit is an assumed condition for the permitting and crediting of stream restoration projects. It is also likely that current understanding of stressors and drivers of stream ecosystem health is insufficient, and that reach-scale restoration focused on geomorphic restoration is not removing the actual sources of stream health impairment that may arise in the upstream watershed. More science could help to identify how to improve the ecological condition of streams through management. The outcome of stream restoration monitoring has revealed that while geomorphic and hydrodynamic functions of stream restoration projects may be achieved, biotic stream function improvements remain elusive. As such, ensuring uplift may be achieved by avoiding restoration projects that risk resources in higher-quality streams and riparian corridors. Reach-scale restoration often does not effectively mitigate the watershed-scale stressors of stream ecosystems. If a desired outcome of stream restoration includes ecological uplift, then focusing efforts on improving stream ecology could help meet that goal.

Chesapeake Bay watershed↗

USGS2007

Development of the Hydroecological Integrity Assessment Process for Determining Environmental Flows for New Jersey Streams

The natural flow regime paradigm and parallel stream ecological concepts and theories have established the benefits of maintaining or restoring the full range of natural hydrologic variation for physiochemical processes, biodiversity, and the evolutionary potential of aquatic and riparian communities. A synthesis of recent advances in hydroecological research coupled with stream classification has resulted in a new process to determine environmental flows and assess hydrologic alteration. This process has national and international applicability. It allows classification of streams into hydrologic stream classes and identification of a set of non-redundant and ecologically relevant hydrologic indices for 10 critical sub-components of flow. Three computer programs have been developed for implementing the Hydroecological Integrity Assessment Process (HIP): (1) the Hydrologic Indices Tool (HIT), which calculates 171 ecologically relevant hydrologic indices on the basis of daily-flow and peak-flow stream-gage data; (2) the New Jersey Hydrologic Assessment Tool (NJHAT), which can be used to establish a hydrologic baseline period, provide options for setting baseline environmental-flow standards, and compare past and proposed streamflow alterations; and (3) the New Jersey Stream Classification Tool (NJSCT), designed for placing unclassified streams into pre-defined stream classes. Biological and multivariate response models including principal-component, cluster, and discriminant-function analyses aided in the development of software and implementation of the HIP for New Jersey. A pilot effort is currently underway by the New Jersey Department of Environmental Protection in which the HIP is being used to evaluate the effects of past and proposed surface-water use, ground-water extraction, and land-use changes on stream ecosystems while determining the most effective way to integrate the process into ongoing regulatory programs. Ultimately, this scientifically defensible process will help to quantify the effects of anthropogenic changes and development on hydrologic variability and help planners and resource managers balance current and future water requirements with ecological needs.

Scientific Investigations Report↗

USGS2004

Comparison of methods for determining streamflow requirements for aquatic habitat protection at selected sites on the Assabet and Charles Rivers, Eastern Massachusetts, 2000-02

Four methods used to determine streamflow requirements for habitat protection at nine critical riffle reaches in the Assabet River and Charles River Basins were compared. The methods include three standard setting techniques?R2Cross, Wetted Perimeter, and Tennant?and a diagnostic method, the Range of Variability Approach. One study reach is on the main stem of the Assabet River, four reaches are on tributaries to the Assabet River (Cold Harbor Brook, Danforth Brook, Fort Meadow Brook, and Elizabeth Brook), three are on the main stem of the Charles River, and one is on a tributary to the Charles River (Mine Brook). The strength of the R2Cross and Wetted-Perimeter methods is that they may be applied at ungaged locations whereas the Tennant method and the Range of Variability Approach require a period of streamflow record for analysis. Fish community assessments conducted at or near riffle sites in flowing reaches of the Assabet River and Charles River Basins were used to indicate ecological conditions. The fish communities in the main stem and tributary reaches of both the Assabet and Charles River Basins indicated degraded aquatic ecosystems. However, the degree of degradation differs between the two basins. The extreme predominance of tolerant, generalist species in the Charles River fish community demon-strates the cumulative impacts of flow, habitat, and water-chemistry degradation, combined with the effects of nearby impoundments and changing land use. The range of discharges for nine ungaged riffle reaches defined by the median R2Cross 3-of-3 criteria, R2Cross 2-of-3 criteria, and Wetted-Perimeter streamflow requirements, was 0.86 cubic foot per second per square mile, 0.18 cubic foot per second per square mile, and 0.23 cubic foot per second per square mile, respectively. Application of R2Cross and Wetted-Perimeter methods to sites with altered streamflows or at sites that are riffles only at low to moderate flows can result in a greater variability of streamflow requirements than would result if the methods were applied to riffles on natural channels with unaltered streamflows. The R2Cross 2-of-3 criteria and the Wetted-Perimeter streamflow requirements for the Assabet and Charles River sites show narrower interquartile ranges and lower median streamflow requirements than for 10 index streamflow-gaging stations in southern New England. This is especially evident for the R2Cross 2-of-3 criteria and Wetted-Perimeter results that were close to half of the flow requirements determined at the 10 southern New England stations. The R2Cross and Wetted-Perimeter methods were also compared to the Range of Variability Approach analysis and the Tennant Method. The median R2Cross 3-of-3 criteria streamflow requirement for the nine riffles is close to the 75th percentile of the monthly mean flows during the summer low-flow period from six streamflow-gaging stations near the Assabet and Charles River Basins having mostly unaltered flow. This streamflow requirement is close to the median Tennant 40-percent-flow requirement for good habitat condi-tion for the same six nearby stations. The R2Cross 2-of-3 criteria and Wetted-Perimeter results were less than the 25th-percentile of monthly mean flows during the summer months for the six stations. These streamflow requirements are in the poor habitat range as indicated by a Tennant analysis of the same six stations. These comparisons indicate that the R2Cross and Wetted-Perimeter methods underestimate streamflow requirements when applied to sites in smaller drainage areas and channels that are runs at higher flows.

Scientific Investigations Report↗

USGS2023

Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex

Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America’s Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia —a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species ( Erimystax dissimilis ) confirmed to serve as a parasitic larval host for P. sintoxia . Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.

Mississippi River basin↗