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Remote monitoring of fish in small streams: A unified approach using PIT tags

Accurate assessments of fish populations are often limited by re-observation or recapture events. Since the early 1990s, passive integrated transponders (PIT tags) have been used to understand the biology of many fish species. Until recently, PIT applications in small streams have been limited to physical recapture events. To maximize recapture probability, we constructed PIT antenna arrays in small streams to remotely detect individual fish. Experiences from two different laboratories (three case studies) allowed us to develop a unified approach to applying PIT technology for enhancing data assessments. Information on equipment, its installation, tag considerations, and array construction is provided. Theoretical and practical definitions are introduced to standardize metrics for assessing detection efficiency. We demonstrate how certain conditions (stream discharge, vibration, and ambient radio frequency noise) affect the detection efficiency and suggest that by monitoring these conditions, expectations of efficiency can be modified. We emphasize the importance of consistently estimating detection efficiency for fisheries applications.

Fisheries

Quality assurance practices for the chemical and biological analyses of water and fluvial sediments

This chapter contains practices used by the U.S. Geological Survey to assure the quality of analytical data for water, fluvial sediment, and aquatic organisms. These practices are directed primarily toward personnel making water quality measurements. Some detail specific quality control techniques, others document quality assurance procedures being used by the Central Laboratories System of the U.S. Geological Survey, and still others describe various statistical techniques and give examples of their use in evaluating and assuring the quality of analytical data. The practices are arranged into eight sections: Analytical Methods Development Procedures, Standard Quantitative Analysis Techniques, Instrumental Techniques, Reference Material, Laboratory Quality Control; Quality Assurance Monitoring; Documentation, Summary, and Evaluation of Data, Materials Evaluation. Each section is preceded by a brief description of the material covered. Similarly within each section, each practice is preceded by a description of its application or scope.

Techniques of Water-Resources Investigations

An isotope-dilution standard GC/MS/MS method for steroid hormones in water

An isotope-dilution quantification method was developed for 20 natural and synthetic steroid hormones and additional compounds in filtered and unfiltered water. Deuterium- or carbon-13-labeled isotope-dilution standards (IDSs) are added to the water sample, which is passed through an octadecylsilyl solid-phase extraction (SPE) disk. Following extract cleanup using Florisil SPE, method compounds are converted to trimethylsilyl derivatives and analyzed by gas chromatography with tandem mass spectrometry. Validation matrices included reagent water, wastewater-affected surface water, and primary (no biological treatment) and secondary wastewater effluent. Overall method recovery for all analytes in these matrices averaged 100%; with overall relative standard deviation of 28%. Mean recoveries of the 20 individual analytes for spiked reagent-water samples prepared along with field samples analyzed in 2009–2010 ranged from 84–104%, with relative standard deviations of 6–36%. Detection levels estimated using ASTM International’s D6091–07 procedure range from 0.4 to 4 ng/L for 17 analytes. Higher censoring levels of 100 ng/L for bisphenol A and 200 ng/L for cholesterol and 3-beta-coprostanol are used to prevent bias and false positives associated with the presence of these analytes in blanks. Absolute method recoveries of the IDSs provide sample-specific performance information and guide data reporting. Careful selection of labeled compounds for use as IDSs is important because both inexact IDS-analyte matches and deuterium label loss affect an IDS’s ability to emulate analyte performance. Six IDS compounds initially tested and applied in this method exhibited deuterium loss and are not used in the final method.

Book chapter

Quality assurance practices for the chemical and biological analyses of water and fluvial sediments

This chapter contains practices used by the U.S. Geological Survey to assure the quality of analytical data for water, fluvial sediment, and aquatic organisms. These practices are directed primarily toward personnel making water-quality measurements. Some detail specific quality control techniques, others document quality assurance procedures being used by the Central Laboratories System of the U.S. Geological Survey, and still others describe various statistical techniques and give examples of their use in evaluating and assuring the quality of analytical data. The practices are arranged into eight sections: Analytical Methods Development Procedures Standard Quantitative Analysis Techniques Instrumental Techniques Reference Material Laboratory Quality Control Quality Assurance Monitoring Documentation, Summary, and Evaluation of Data Materials Evaluation Each section is preceded by a brief description of the material covered. Similarly within each section, each practice is preceded by a description of its application or scope.

Open-File Report

Predictive models for fish assemblages in eastern USA streams: implications for assessing biodiversity

Management and conservation of aquatic systems require the ability to assess biological conditions and identify changes in biodiversity. Predictive models for fish assemblages were constructed to assess biological condition and changes in biodiversity for streams sampled in the eastern United States as part of the U.S. Geological Survey's National Water Quality Assessment Program. Separate predictive models were developed for northern and southern regions. Reference sites were designated using land cover and local professional judgment. Taxonomic completeness was quantified based on the ratio of the number of observed native fish species expected to occur to the number of expected native fish species. Models for both regions accurately predicted fish species composition at reference sites with relatively high precision and low bias. In general, species that occurred less frequently than expected (decreasers) tended to prefer riffle areas and larger substrates, such as gravel and cobble, whereas increaser species (occurring more frequently than expected) tended to prefer pools, backwater areas, and vegetated and sand substrates. In the north, the percentage of species identified as increasers and the percentage identified as decreasers were equal, whereas in the south nearly two-thirds of the species examined were identified as decreasers. Predictive models of fish species can provide a standardized indicator for consistent assessments of biological condition at varying spatial scales and critical information for an improved understanding of fish species that are potentially at risk of loss with changing water quality conditions.

Transactions of the American Fisheries Society

Nature's Notebook 2011: Data & participant summary

Introduction The USA National Phenology Network The USA National Phenology Network (USA‐NPN; www.usanpn.org) seeks to engage a diverse range of citizen scientist volunteers, federal, state, and non‐governmental organizations, educators and professional research scientists to collect phenological observations of plants and animals using consistent standards and to contribute their observations to a national data repository. To guide this effort, the USA‐NPN National Coordinating Office (NCO), based in Tucson, Arizona, implemented an online monitoring program for plants and animals, Nature's Notebook , and has developed phenology monitoring protocols and an information management system, which includes the National Phenology Database (NPDb). We are developing a diversity of materials, tools, techniques, and protocols to assist decision making and education related to ecology, wildlife, human health, ecosystem services, natural resource management, biological conservation, and climate change adaptation.

USA-NPN Technical Series

Flow cytometric detection of waterborne bacteria metabolic response to anthropogenic chemical inputs to aquatic ecosystems

Typical investigations into the biological consequences of suspected xenobiotics or nutrients introduced in watersheds include analytical chemistry screens of environmental samples—such as periphyton responses or studies of fish condition—which are all costly in terms of equipment, reagents, time, and human resources. An alternative is to assess pollutant effects on waterborne bacteria. A flow cytometric method was developed to yield rapid, same-day results that could be used to proactively screen for suspected chemical inputs into watersheds using water sampling methods that are identical to those in standard use. The analytical methods are microbe cultivation-independent, for use with waterborne bacteria that are typically viable but not culturable. The procedure is quick and inexpensive, generating measures of bacterial esterase that reflect metabolic activity and are sensitive and statistically robust. After phosphate-EDTA incubation to increase cell wall permeability, staining was performed with 5(6) carboxyfluorescein diacetate (enzyme activity) and propidium iodide (cell viability) with three bacterial species in exponential phase growth having been incubated with organic wastewater compounds (atrazine, pharmaceuticals [17α-ethynylestradiol and trenbolone], and antimicrobials [tylosin and butylparaben]). This method successfully detected metabolic changes in all bacterial species, with atrazine inducing the greatest change. Additional fluorescent stains can target specific microbial structures or functions of interest in a particular watershed. This biotechnology can inform analytical chemistry and study of biota at sites of interest and has the potential to be automated.

Cells

An interactive decision-making tool for evaluating biological and statistical standards of migrating fish survival past hydroelectric dams

Quantifying the downstream survival of migrating fish past dams is critical for conservation efforts. Regulators require assessments of survival as a condition of operation. Failure to meet an established survival standard may result in required operational or costly structural changes at a facility. Establishing the survival standard, as well as the rules of assessment, is a point of contention between regulators and operators. Management goals are based on biological criteria, but there are inherent statistical and probabilistic trade-offs when choosing a standard value and the method for assessment. We make a distinction between a “biological” goal (the conservation goal) and a “statistical” standard (a function of the biological goal, sample size, assessment method, and years of consecutive evaluation). An effective statistical standard maximizes true positives (passing the standard when the biological goal is being met) and true negatives (failing the standard when the goal is not being met), while minimizing false negatives and false positives. We explored the effects of sample size, true survival, and assessment methods on the probability of passing different statistical standards by simulating survival studies (simulating mark-recapture experiments). We observed a strong influence of assessment methods on the probability of making the right decision (true positive or true negative), especially when sample size, and recapture probability was low. As a support tool, we developed an interactive user interface to explore specific scenarios, and to aid communication among decision-makers.

River Research and Applications

Trends in marine debris in the U.S. Caribbean and the Gulf of Mexico, 1996-2003

Marine debris is a widespread and globally recognized problem. Sound information is necessary to understand the extent of the problem and to inform resource managers and policy makers about potential mitigation strategies. Although there are many short-term studies on marine debris, a longer-term perspective and the ability to compare among regions has heretofore been missing in the U.S. Caribbean and the Gulf of Mexico. We used data from a national beach monitoring program to evaluate and compare amounts, composition, and trends of indicator marine debris in the U.S. Caribbean (Puerto Rico and the U.S. Virgin Islands) and the Gulf of Mexico from 1996 to 2003. Indicator items provided a standardized set that all surveys collected; each was assigned a probable source: ocean-based, land-based, or general-source. Probable ocean-based debris was related to activities such as recreational boating/fishing, commercial fishing and activities on oil/gas platforms. Probable land-based debris was related to land-based recreation and sewer systems. General-source debris represented plastic items that can come from either ocean- or land-based sources; these items were plastic bags, strapping bands, and plastic bottles (excluding motor oil containers). Debris loads were similar between the U.S. Caribbean and the western Gulf of Mexico; however, debris composition on U.S. Caribbean beaches was dominated by land-based indicators while the western Gulf of Mexico was dominated by ocean-based indicators. Beaches along the eastern Gulf of Mexico had the lowest counts of debris; composition was dominated by land-based indicators, similar to that found for the U.S. Caribbean. Debris loads on beaches in the Gulf of Mexico are likely affected by Gulf circulation patterns, reducing loads in the eastern Gulf and increasing loads in the western Gulf. Over the seven years of monitoring, we found a large linear decrease in total indicator debris, as well as all source categories, for the U.S. Caribbean. Lower magnitude decreases were seen in indicator debris along the eastern Gulf of Mexico. In contrast, only land-based indicators declined in the western Gulf of Mexico; total, ocean-based and general-source indicators remained unchanged. Decreases in land-based indicators were not related to human population in the coastal regions; human population increased in all regions over the time of the study. Significant monthly patterns for indicator debris were found only in the Gulf of Mexico; counts were highest during May through September, with peaks occurring in July. Inclement weather conditions before the time of the survey also accounted for some of the variation in the western Gulf of Mexico; fewer items were found when there were heavy seas or cold fronts in the weeks prior to the survey, while tropical storms (including hurricanes) increased the amount of debris. With the development around the globe of long-term monitoring programs using standardized methodology, there is the potential to help management at individual sites, as well as generate larger-scale perspectives (from regional to global) to inform decision makers. Incorporating mechanisms producing debris into marine debris programs would be a fruitful area for future research.

Gulf of Mexico and U.S. Carribean

Minimizing effects of methodological decisions on interpretation and prediction in species distribution studies: An example with background selection

Evaluating the conditions where a species can persist is an important question in ecology both to understand tolerances of organisms and to predict distributions across landscapes. Presence data combined with background or pseudo-absence locations are commonly used with species distribution modeling to develop these relationships. However, there is not a standard method to generate background or pseudo-absence locations, and method choice affects model outcomes. We evaluated combinations of both model algorithms (simple and complex generalized linear models, multivariate adaptive regression splines, Maxent, boosted regression trees, and random forest) and background methods (random, minimum convex polygon, and continuous and binary kernel density estimator (KDE)) to assess the sensitivity of model outcomes to choices made. We evaluated six questions related to model results, including five beyond the common comparison of model accuracy assessment metrics (biological interpretability of response curves, cross-validation robustness, independent data accuracy and robustness, and prediction consistency). For our case study with cheatgrass in the western US, random forest was least sensitive to background choice and the binary KDE method was least sensitive to model algorithm choice. While this outcome may not hold for other locations or species, the methods we used can be implemented to help determine appropriate methodologies for particular research questions.

Ecological Modelling

Resilience and risk: a demographic model to inform conservation planning for polar bears

Climate change is having widespread ecological effects, including loss of Arctic sea ice. This has led to listing of the polar bear ( Ursus maritimus ) and other ice-dependent marine mammals under the U.S. Endangered Species Act (ESA). Methods are needed to evaluate the effects of climate change on population persistence to inform recovery planning for listed species. For polar bears, this includes understanding interactions between climate and secondary factors, such as subsistence harvest, which provide economic, nutritional, or cultural value to humans. We developed a matrix-based demographic model for polar bears that can be used for population viability analysis and to evaluate the effects of human-caused removals. This model includes density-dependence (the potential for a declining environmental carrying capacity), density-independent limitation, and sex- and age-specific harvest vulnerabilities. We estimated values of adult female survival (0.93–0.96), recruitment (number of yearling cubs per adult female; 0.1–0.3), and carrying capacity (>250 animals) that must be maintained for a hypothetical population to achieve a 90-percent probability of persistence over 100 years. We also developed a state-dependent management framework, based on harvest theory and the potential biological removal method, by linking the demographic model to simulated population assessments. This framework can be used to estimate the maximum sustainable rate of human-caused removals, including subsistence harvest, which maintains a population at its maximum net productivity level. The framework also can be used to calculate a recommended sustainable harvest rate, which generally is lower than the maximum sustainable rate and depends on management objectives, the precision and frequency of population data, and risk tolerance. The historical standard 4.5-percent harvest rate for polar bears, at a 2:1 male-to-female ratio, is reasonable under many biological and management conditions, although lower or higher rates may be appropriate in some cases. Our modeling results suggest that harvest of polar bears is unlikely to accelerate population declines that result from declining carrying capacity caused by sea-ice loss, provided that several conditions are met: (1) the sustainable harvest rate reflects the population’s intrinsic growth rate, and the corresponding harvest level is obtained by applying this rate to an estimate of population size; (2) the sustainable harvest rate reflects the quality of population data (e.g., lower harvest when data are poor); and (3) the level of human-caused removals can be adjusted. Finally, our results suggest that stopgap measures (e.g., further reduction or cessation of harvest when the population size is less than a critical threshold) may be necessary to minimize the incremental risk associated with harvest, if environmental conditions are deteriorating rapidly. We suggest that the demographic model and approaches presented here can serve as a template for conservation planning for polar bears and other species facing similar challenges.

Open-File Report

National Park Service Vegetation Inventory Program, Cuyahoga Valley National Park, Ohio

The National Park Service (NPS) Vegetation Inventory Program (VIP) is an effort to classify, describe, and map existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VIP is managed by the NPS Biological Resources Management Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey (USGS) Vegetation Characterization Program lends a cooperative role in the NPS VIP. The USGS Upper Midwest Environmental Sciences Center, NatureServe, and NPS Cuyahoga Valley National Park (CUVA) have completed vegetation classification and mapping of CUVA. Mappers, ecologists, and botanists collaborated to identify and describe vegetation types within the National Vegetation Classification Standard (NVCS) and to determine how best to map them by using aerial imagery. The team collected data from 221 vegetation plots within CUVA to develop detailed descriptions of vegetation types. Data from 50 verification sites were also collected to test both the key to vegetation types and the application of vegetation types to a sample set of map polygons. Furthermore, data from 647 accuracy assessment (AA) sites were collected (of which 643 were used to test accuracy of the vegetation map layer). These data sets led to the identification of 45 vegetation types at the association level in the NVCS at CUVA. A total of 44 map classes were developed to map the vegetation and general land cover of CUVA, including the following: 29 map classes represent natural/semi-natural vegetation types in the NVCS, 12 map classes represent cultural vegetation (agricultural and developed) in the NVCS, and 3 map classes represent non-vegetation features (open-water bodies). Features were interpreted from viewing color-infrared digital aerial imagery dated October 2010 (during peak leaf-phenology change of trees) via digital onscreen three-dimensional stereoscopic workflow systems in geographic information systems (GIS). The interpreted data were digitally and spatially referenced, thus making the spatial database layers usable in GIS. Polygon units were mapped to either a 0.5 ha or 0.25 ha minimum mapping unit, depending on vegetation type. A geodatabase containing various feature-class layers and tables shows the locations of vegetation types and general land cover (vegetation map), vegetation plot samples, verification sites, AA sites, project boundary extent, and aerial photographic centers. The feature-class layer and relate tables for the CUVA vegetation map provides 4,640 polygons of detailed attribute data covering 13,288.4 ha, with an average polygon size of 2.9 ha. Summary reports generated from the vegetation map layer show map classes representing natural/semi-natural types in the NVCS apply to 4,151 polygons (89.4% of polygons) and cover 11,225.0 ha (84.5%) of the map extent. Of these polygons, the map layer shows CUVA to be 74.4% forest (9,888.8 ha), 2.5% shrubland (329.7 ha), and 7.6% herbaceous vegetation cover (1,006.5 ha). Map classes representing cultural types in the NVCS apply to 435 polygons (9.4% of polygons) and cover 1,825.7 ha (13.7%) of the map extent. Map classes representing non-NVCS units (open water) apply to 54 polygons (1.2% of polygons) and cover 237.7 ha (1.8%) of the map extent. A thematic AA study was conducted of map classes representing natural/semi-natural types in the NVCS. Results present an overall accuracy of 80.7% (kappa index of 79.5%) based on data from 643 of the 647 AA sites. Most individual map-class themes exceed the NPS VIP standard of 80% with a 90% confidence interval. The CUVA vegetation mapping project delivers many geospatial and vegetation data products in hardcopy and/or digital formats. These products consist of an in-depth project report discussing methods and results, which include descriptions and a dichotomous key to vegetation types, map classification and map-class descriptions, and a contingency table showing AA results. The suite of products also includes a database of vegetation plots, verification sites, and AA sites; digital pictures of field sites; field data sheets; aerial photographic imagery; hardcopy and digital maps; and a geodatabase of vegetation types and land cover (map layer), fieldwork locations (vegetation plots, verification sites, and AA sites), aerial photographic index, project boundary, and metadata. All geospatial products are projected in Universal Transverse Mercator, Zone 17, by using the North American Datum of 1983. Information on the NPS VIP and completed park mapping projects are located on the Internet at <http://science.nature.nps.gov/im/inventory/veg> and <http://www.usgs.gov/core_science_systems/csas/vip/index.html>.

Natural Resource Technical Report

High-precision measurement of variations in calcium isotope ratios in urine by multiple collector inductively coupled plasma mass spectrometry

We describe a new chemical separation method to isolate Ca from other matrix elements in biological samples, developed with the long-term goal of making high-precision measurement of natural stable Ca isotope variations a clinically applicable tool to assess bone mineral balance. A new two-column procedure utilizing HBr achieves the purity required to accurately and precisely measure two Ca isotope ratios ( 44 Ca/ 42 Ca and 44 Ca/ 43 Ca) on a Neptune multiple collector inductively coupled plasma mass spectrometer (MC-ICPMS) in urine. Purification requirements for Sr, Ti, and K (Ca/Sr > 10000; Ca/Ti > 10000000; and Ca/K > 10) were determined by addition of these elements to Ca standards of known isotopic composition. Accuracy was determined by (1) comparing Ca isotope results for samples and standards to published data obtained using thermal ionization mass spectrometry (TIMS), (2) adding a Ca standard of known isotopic composition to a urine sample purified of Ca, and (3) analyzing mixtures of urine samples and standards in varying proportions. The accuracy and precision of &delta; 44/42 Ca measurements of purified samples containing 25 &mu;g of Ca can be determined with typical errors less than &plusmn;0.2&permil; (2&sigma;).

Analytical Chemistry

Realizing the potential of eDNA biodiversity monitoring tools in the marine environment with application to offshore renewable energy

The U.S. Geological Survey (USGS) researches the biological diversity and distribution of species to support management, conservation, and resource use decisions. USGS scientists advance detection and monitoring technologies to assess changes in fish and wildlife populations, biodiversity, and the health of ecosystems. The United States is planning to install 30 gigawatts of offshore marine and wind energy by 2030. However, the effects on fish and wildlife and their habitats are not well understood. The USGS is a leader in the field of eDNA technologies and has helped advance robotic eDNA samplers, has extensive experience working in the offshore environment, and has developed novel and actionable statistical methods and standards for eDNA monitoring applications. This fact sheet presents key eDNA research and development advances needed for realizing the potential of eDNA biodiversity monitoring tools in the marine environment and applying eDNA monitoring to offshore renewable energy development. New and cost-effective tools for measuring changes in biodiversity in response to offshore renewable energy development can help to inform natural resource management and project planning and permitting decisions.

Fact Sheet

A proposed international watershed research network

An “International Watershed Research Network” is to be an initial project of the Sino-U. S. Centers for Soil and Water Conservation and Environmental Protection. The Network will provide a fundamental database for research personnel of the Centers, as well as of the global research community, and is viewed as an important resource for their successful operation. Efforts are under way to (a) identify and select candidate watersheds, (b) develop standards and protocols for data collection and dissemination, and (c) specify other data sources on erosion, sediment transport, hydrology, and ancillary information of probable interest and use to participants of the Centers. The initial focus of the Network will be on water-deficient areas. Candidate watersheds for the Network are yet to be determined although likely selections include the Ansai Research Station, northern China, and the Walnut Gulch Experimental Watershed, Arizona, USA. The Network is to be patterned after the Vigil Network, an open-ended group of global sites and small drainage basins for which Internet-accessible geomorphic, hydrologic, and biological data are periodically collected or updated. Some types of data, using similar instruments and observation methods, will be collected at all watersheds selected for the Network. Other data from the watersheds that may reflect individual watershed characteristics and research objectives will be collected as well.

Conference Paper

Fitting a structured juvenile-adult model for green tree frogs to population estimates from capture-mark-recapture field data

We derive point and interval estimates for an urban population of green tree frogs ( Hyla cinerea ) from capture–mark–recapture field data obtained during the years 2006–2009. We present an infinite-dimensional least-squares approach which compares a mathematical population model to the statistical population estimates obtained from the field data. The model is composed of nonlinear first-order hyperbolic equations describing the dynamics of the amphibian population where individuals are divided into juveniles (tadpoles) and adults (frogs). To solve the least-squares problem, an explicit finite difference approximation is developed. Convergence results for the computed parameters are presented. Parameter estimates for the vital rates of juveniles and adults are obtained, and standard deviations for these estimates are computed. Numerical results for the model sensitivity with respect to these parameters are given. Finally, the above-mentioned parameter estimates are used to illustrate the long-time behavior of the population under investigation.

Bulletin of Mathematical Biology

A systematic literature review of forecasting and predictive models of harmful algal blooms in flowing waters

Occurrences of harmful algal blooms (HABs) in rivers challenge the belief that rivers are not susceptible to HABs because of their short residence times and fluctuating hydrology. Here we present a systematic literature review of predictive and forecasting models for HABs in flowing waters, including rivers, flowing in-stream reservoirs (e.g., run-of-river reservoirs and lock-and-dam systems) and tidal or estuarine systems with riverine processes. The review aimed to understand current and historical modeling approaches for predicting and forecasting river HABs, without restricting to specific taxa, such as cyanobacteria, or modeling endpoints. The review included 162 articles published over nearly 50 years, covering more than 80 rivers worldwide. Eutrophic, non-wadable rivers with in-stream obstruction were commonly modeled, though diverse environmental characteristics were reported. Most articles used algal biomass or chlorophyll as modeling endpoints, with a quarter using novel or unique endpoints. Algal toxins motivated model development in 23% of the articles, however just 5% used algal toxins as an endpoint. Only 6% of the articles modeled benthic HABs; the rest focused on pelagic HABs. There was no standard model used for modeling river HABs. Process-based models were more common (59%) than data-driven approaches (37%), with model formulations ranging from simple to complex, which contrasts with a lake-focused literature review of HAB models that found data-driven models were more common. Models in river settings shared similar input variables as those previously identified for lakes, such as water temperature, nutrients, and light availability. However, streamflow and other transport metrics took prominence in river models compared to lake models. Algal cell physiology (such as growth, predation, and motility) was routinely included as input data or as mathematical formulations in process-based models and these processes were frequently identified as an important predictor by the articles’ authors. Conversely, data-driven models rarely included these processes, instead using predictors related to environmental conditions, such as nutrients, water quality, water temperature, and streamflow. These important proxy predictors have apparent success with modeling overall algal biomass (irrespective of taxa) whereas other factors, such as those related to algal physiology and other biological processes, are likely responsible for more subtle shifts in community composition. These differences highlight the influence of data availability, especially for processes that are difficult, time-consuming, or expensive to measure, on model development and model outcomes, raising questions about the selection of modeling inputs and endpoints. Challenges to advancing river HAB modeling include the lack of site-specific model inputs representing key processes (e.g., photosynthetic parameters and predation rates), overlooked riverine environments like the benthos and side/back-channel areas, lack of information on environmental settings, and poorly reported model performance metrics. This review emphasizes opportunities for advancing river HAB modeling by learning from well-honed estuarine models, supporting current forecasting and operationalization efforts, and developing common datasets for river HAB model development and evaluation.

BioRxiv

Water-quality, biological, and physical-habitat conditions at fixed sites in the Cook Inlet Basin, Alaska, National Water-Quality Assessment Study Unit, October 1998-September 2001

The Cook Inlet Basin study unit of the U.S. Geological Survey National Water-Quality Assessment Program comprises 39,325 square miles in south-central Alaska. Data were collected at eight fixed sites to provide baseline information in areas where no development has taken place, urbanization or logging have occurred, or the effects of recreation are increasing. Collection of water-quality, biology, and physical-habitat data began in October 1998 and ended in September 2001 (water years 1999-2001). The climate for the water years in the study may be categorized as slightly cool-wet (1999), slightly warm-wet (2000), and significantly warm-dry (2001). Total precipitation was near normal during the study period, and air temperatures ranged from modestly cool in water year 1999 to near normal in 2000, and to notably warm in 2001. Snowmelt runoff dominates the hydrology of streams in the Cook Inlet Basin. Average annual flows at the fixed sites were approximately the same as the long-term average annual flows, with the exception of those in glacier-fed basins, which had above-average flow in water year 2001. Water temperature of all streams studied in the Cook Inlet Basin remained at 0 oC for about 6 months per year, and average annual water temperatures ranged from 3.3 to 6.2 degrees Celsius. Of the water-quality constituents sampled, all concentrations were less than drinking-water standards and only one constituent, the pesticide carbaryl, exceeded aquatic-life standards. Most of the stream waters of the Cook Inlet Basin were classified as calcium bicarbonate, which reflects the underlying geology. Streams in the Cook Inlet Basin draining areas with glaciers, rough mountainous terrain, and poorly developed soils have low concentrations of nitrogen, phosphorus, and dissolved organic carbon compared with concentrations of these same constituents in streams in lowland or urbanized areas. In streams draining relatively low-lying areas, most of the suspended sediment, nutrients, and dissolved organic carbon are transported in the spring from the melting snowpack. The urbanized stream, Chester Creek, had the highest concentrations of calcium, magnesium, chloride, and sodium, most likely because of the application of de-icing materials during the winter. Several volatile organic compounds and pesticides also were detected in samples from this stream. Aquatic communities in the Cook Inlet Basin are naturally different than similar sites in the contiguous United States because of the unique conditions of the northern latitudes where the Cook Inlet Basin is located, such as extreme diurnal cycles and long periods of ice cover. Blue-green algae was the dominant algae found at all sites although in some years green algae was the most dominant algae. Macroinvertebrate communities consist primarily of Diptera (true flies), Ephemeroptera (mayflies), and Plecoptera (stoneflies). Lowland areas have higher abundance of aquatic communities than glacier-fed basins. However, samples from the urbanized stream, Chester Creek, were dominated by oligochaetes, a class of worms. Most of the functional feeding groups were collector-gatherers. The number of taxa for both algae and macroinvertebrates were highest in water year 2001, which may be due to the relative mild winter of 2000?2001 and the above average air temperatures for this water year. The streams in the Cook Inlet Basin typically are low gradient. Bank substrates consist of silt, clay, or sand, and bed substrate consists of coarse gravel or cobbles. Vegetation is primarily shrubs and woodlands with spruce or cottonwood trees. Canopy angles vary with the size of the stream or river and are relatively low at the smaller streams and high at the larger streams. Suitable fish habitat, such as woody debris, pools, cobble substrate, and overhanging vegetation, is found at most sites. Of the human activities occurring in the fixed site basins ? high recreational use, logging, and urbanizat

Scientific Investigations Report