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Climate and dispersal ability limit future habitats for Gila monsters in the Mojave Desert

Describing future habitat for sensitive species can be helpful in planning conservation efforts to ensure species persistence under new climatic conditions. The Gila monster ( Heloderma suspectum ) is an iconic lizard of the southwestern United States. The northernmost range of Gila monsters is the Mojave Desert, an area experiencing rapid human population growth and urban sprawl. To understand current and potential future habitat for Gila monsters in the Mojave Desert, we fit ensemble species distribution models using known locations and current environmental variables known to be important to the species' biology. We then projected future suitable habitat under different climate forecasts based on IPCC emission scenarios. To ensure that Gila monsters would be able to disperse to newly suitable habitat, we fit Brownian Bridge movement models using telemetry data from two locations in Nevada. This model indicated that Gila monsters prefer to move through areas with a moderate slope and higher shrub cover. Modeled current suitable habitat for Gila monsters in Nevada was primarily in rugged bajadas and lower elevations at the bases of mountain ranges. Predictions of potential future habitat suggested that overall habitat suitability through 2082 would remain relatively stable throughout the study area in the lower emissions scenario, but in the high emissions scenario potential habitat is greatly reduced in many lower-elevation areas. Future habitat areas at higher elevations under the high emissions scenario showed moderate increases in suitability, though occupancy would likely be limited by Gila monster dispersal capabilities. Finally, we determined how well the protected area network of our study area encompassed future Gila monster habitat to highlight potential opportunities to protect this important species.

Arizona, California, Nevada, Utah

Pesticides in stream sediment and aquatic biota— Current understanding of distribution and major influences

This report summarizes a comprehensive analysis of existing information on pesticides in bed sediment and aquatic biota of United States rivers and streams: their geographic distribution, sources, trends, environmental fate, and biological significance. It is one of a four-part series that synthesizes current knowledge and understanding of pesticides in the nation’s water resources as part of the National Water-Quality Assessment Program.

Fact Sheet

Development of a species status assessment process for decisions under the U.S. Endangered Species Act

Decisions under the U.S. Endangered Species Act (ESA) require scientific input on the risk that the species will become extinct. A series of critiques on the role of science in ESA decisions have called for improved consistency and transparency in species risk assessments and clear distinctions between science input and policy application. To address the critiques and document the emerging practice of the U.S. Fish and Wildlife Service (USFWS), we outline an assessment process based on principles and practices of risk and decision analyses that results in a scientific report on species status. The species status assessment (SSA) process has three successive stages: 1) document the life history and ecological relationships of the species in question to provide the foundation for the assessment, 2) describe and hypothesize causes for the current condition of the species, and 3) forecast the species' future condition. The future condition refers to the ability of a species to sustain populations in the wild under plausible future scenarios. The scenarios help explore the species' response to future environmental stressors and to assess the potential for conservation to intervene to improve its status. The SSA process incorporates modeling and scenario planning for prediction of extinction risk and applies the conservation biology principles of representation, resiliency, and redundancy to evaluate the current and future condition. The SSA results in a scientific report distinct from policy application, which contributes to streamlined, transparent, and consistent decision-making and allows for greater technical participation by experts outside of the USFWS, for example, by state natural resource agencies. We present two case studies based on assessments of the eastern massasauga rattlesnake Sistrurus catenatus and the Sonoran Desert tortoise Gopherus morafkai to illustrate the process. The SSA builds upon the past threat-focused assessment by including systematic and explicit analyses of a species' future response to stressors and conservation, and as a result, we believe it provides an improved scientific analysis for ESA decisions.

Journal of Fish and Wildlife Management

Contaminants of emerging concern presence and adverse effects in fish: A case study in the Laurentian Great Lakes

The Laurentian Great Lakes are a valuable natural resource that is affected by contaminants of emerging concern (CECs), including sex steroid hormones, personal care products, pharmaceuticals, industrial chemicals, and new generation pesticides. However, little is known about the fate and biological effects of CECs in tributaries to the Great Lakes. In the current study, 16 sites on three rivers in the Great Lakes basin (Fox, Cuyahoga, and Raquette Rivers) were assessed for CEC presence using polar organic chemical integrative samplers (POCIS) and grab water samplers. Biological activity was assessed through a combination of in vitro bioassays (focused on estrogenic activity) and in vivo assays with larval fathead minnows. In addition, resident sunfish, largemouth bass, and white suckers were assessed for changes in biological endpoints associated with CEC exposure. CECs were present in all water samples and POCIS extracts. A total of 111 and 97 chemicals were detected in at least one water sample and POCIS extract, respectively. Known estrogenic chemicals were detected in water samples at all 16 sites and in POCIS extracts at 13 sites. Most sites elicited estrogenic activity in bioassays. Ranking sites and rivers based on water chemistry, POCIS chemistry, or total in vitro estrogenicity produced comparable patterns with the Cuyahoga River ranking as most and the Raquette River as least affected by CECs. Changes in biological responses grouped according to physiological processes, and differed between species but not sex. The Fox and Cuyahoga Rivers often had significantly different patterns in biological response Our study supports the need for multiple lines of evidence and provides a framework to assess CEC presence and effects in fish in the Laurentian Great Lakes basin.

Environmental Pollution

Temporal change in biological community structure in the Fountain Creek basin, Colorado, 2001-2008

In 2001, the U.S. Geological Survey, in cooperation with Colorado Springs City Engineering, began a study to better understand the relations between environmental characteristics and biological communities in the Fountain Creek basin in order to aide water-resource management and guide future monitoring activities. To accomplish this task, environmental (streamflow, habitat, and water chemistry) and biological (fish and macroinvertebrate) data were collected annually at 24 sites over a 6- or 8-year period (fish, 2003 to 2008; macroinvertebrates, 2001 to 2008). For this report, these data were first analyzed to determine the presence of temporal change in macroinvertebrate and fish community structure among years using nonparametric multivariate statistics. Where temporal change in the biological communities was found, these data were further analyzed using additional nonparametric multivariate techniques to determine which subset of selected streamflow, habitat, or water-chemistry variables best described site-specific changes in community structure relative to a gradient of urbanization. This study identified significant directional patterns of temporal change in macroinvertebrate and fish community structure at 15 of 24 sites in the Fountain Creek basin. At four of these sites, changes in environmental variables were significantly correlated with the concurrent temporal change identified in macroinvertebrate and fish community structure (Monument Creek above Woodmen Road at Colorado Springs, Colo.; Monument Creek at Bijou Street at Colorado Springs, Colo.; Bear Creek near Colorado Springs, Colo.; Fountain Creek at Security, Colo.). Combinations of environmental variables describing directional temporal change in the biota appeared to be site specific as no single variable dominated the results; however, substrate composition variables (percent substrate composition composed of sand, gravel, or cobble) collectively were present in 80 percent of the environmental variable subsets that were significantly correlated with temporal change in the macroinvertebrate and fish community structure. Other important environmental variables related to temporal change in the biological community structure included those describing channel form (streambank height) and streamflow (normalized annual mean daily flow, high flood-pulse count). Site-specific results from this study were derived from a relatively small number of observations (6 or 8 years of data); therefore, additional years of data may reveal other sites with temporal change in biological community structure, or could define stronger and more consistent linkages between environmental variables and observed temporal change. Likewise current variable subsets could become weaker. Nonetheless, there were several sites where temporal change was detected in this study that could not be explained by the available environmental variables studied herein. Modification of current data-collection activities may be necessary to better understand site-specific temporal relations between biological communities and environmental variables.

Scientific Investigations Report

Invasive plants and their ecological strategies: Prediction and explanation of woody plant invasion in New England

Effective management of introduced species requires the early identification of species that pose a significant threat of becoming invasive. To better understand the invasive ecology of species in New England, USA, we compiled a character data set with which to compare non-native species that are known invaders to non-native species that are not currently known to be invasive. In contrast to previous biological trait-based models, we employed a Bayesian hierarchical analysis to identify sets of plant traits associated with invasiveness for each of three growth forms (vines, shrubs, and trees). The resulting models identify a suite of 'invasive traits' highlighting the ecology associated with invasiveness for each of three growth forms. The most effective predictors of invasiveness that emerged from our model were 'invasive elsewhere', 'fast growth rate', 'native latitudinal range', and 'growth form'. The contrast among growth forms was pronounced. For example, 'wind dispersal' was positively correlated with invasiveness in trees, but negatively correlated in shrubs and vines. The predictive model was able to correctly classify invasive plants 67% of the time (22/33), and non-invasive plants 95% of the time (204/215). A number of potential future invasive species in New England that deserve management consideration were identified. ?? 2007 The Authors.

Diversity and Distributions

A Study of the Connection Among Basin-Fill Aquifers, Carbonate-Rock Aquifers, and Surface-Water Resources in Southern Snake Valley, Nevada

The Secretary of the Interior through the Southern Nevada Public Lands Management Act approved funding for research to improve understanding of hydrologic systems that sustain numerous water-dependent ecosystems on Federal lands in Snake Valley, Nevada. Some of the streams and spring-discharge areas in and adjacent to Great Basin National Park have been identified as susceptible to ground-water withdrawals (Elliott and others, 2006) and research has shown a high potential for ground-water flow from southern Spring Valley into southern Snake Valley through carbonate rocks that outcrop along a low topographic divide known as the Limestone Hills (Welch and others, 2007). Comprehensive geologic, hydrologic, and chemical information will be collected and analyzed to assess the hydraulic connection between basin-fill aquifers and surface-water resources, water-dependent ecological features, and the regional carbonate-rock aquifer, the known source of many high-discharge springs. Understanding these connections is important because proposed projects to pump and export ground water from Spring and Snake Valleys in Nevada may result in unintended capture of water currently supplying springs, streams, wetlands, limestone caves, and other biologically sensitive areas (fig. 1). The methods that will be used in this study may be transferable to other areas in the Great Basin. The National Park Service, Bureau of Land Management, U.S. Fish and Wildlife Service, and U.S. Forest Service submitted the proposal for funding this research to facilitate science-based land management. Scientists from the U.S. Geological Survey (USGS) Water Resources and Geologic Disciplines, and the University of Nevada, Reno, will accomplish four research elements through comprehensive data collection and analysis that are concentrated in two distinct areas on the eastern and southern flanks of the Snake Range (fig. 2). The projected time line for this research is from July 2008 through September 2011.

Fact Sheet

Mapping habitat for multiple species in the Desert Southwest

Many utility scale renewable energy projects are currently proposed across the Mojave Ecoregion. Agencies that manage biological resources throughout this region need to understand the potential impacts of these renewable energy projects and their associated infrastructure (for example, transmission corridors, substations, access roads, etc.) on species movement, genetic exchange among populations, and species’ abilities to adapt to changing environmental conditions. Understanding these factors will help managers’ select appropriate project sites and possibly mitigate for anticipated effects of management activities. We used species distribution models to map habitat for 15 species across the Mojave Ecoregion to aid regional land-use management planning. Models were developed using a common 1 × 1 kilometer resolution with maximum entropy and generalized additive models. Occurrence data were compiled from multiple sources, including VertNet ( http://vertnet.org/ ), HerpNET ( http://www.herpnet.org ), and MaNIS ( http://manisnet.org ), as well as from internal U.S. Geological Survey databases and other biologists. Background data included 20 environmental covariates representing terrain, vegetation, and climate covariates. This report summarizes these environmental covariates and species distribution models used to predict habitat for the 15 species across the Mojave Ecoregion.

Mojave Ecoregion

Titanium

Titanium is a mineral commodity that is essential to the smooth functioning of modern industrial economies. Most of the titanium produced is refined into titanium dioxide, which has a high refractive index and is thus able to impart a durable white color to paint, paper, plastic, rubber, and wallboard. Because of their high strength-to-weight ratio and corrosion resistance, titanium metal and titanium metal alloys are used in the aerospace industry as well as for welding rod coatings, biological implants, and consumer goods. Ilmenite and rutile are currently the principal titanium-bearing ore minerals, although other minerals, including anatase, perovskite, and titanomagnetite, could have economic importance in the future. Ilmenite is currently being mined from two large magmatic deposits hosted in rocks of Proterozoic-age anorthosite plutonic suites. Most rutile and nearly one-half of the ilmenite produced are from heavy-mineral alluvial, fluvial, and eolian deposits. Titanium-bearing minerals occur in diverse geologic settings, but many of the known deposits are currently subeconomic for titanium because of complications related to the mineralogy or because of the presence of trace contaminants that can compromise the pigment production process. Global production of titanium minerals is currently dominated by Australia, Canada, Norway, and South Africa; additional amounts are produced in Brazil, India, Madagascar, Mozambique, Sierra Leone, and Sri Lanka. The United States accounts for about 4 percent of the total world production of titanium minerals and is heavily dependent on imports of titanium mineral concentrates to meet its domestic needs. Titanium occurs only in silicate or oxide minerals and never in sulfide minerals. Environmental considerations for titanium mining are related to waste rock disposal and the impact of trace constituents on water quality. Because titanium is generally inert in the environment, human health risks from titanium and titanium mining are minimal; however, the processes required to extract titanium from titanium feedstock can produce industrial waste.

Professional Paper

Relation of urbanization to stream habitat and geomorphic characteristics in nine metropolitan areas of the United States

The relation of urbanization to stream habitat and geomorphic characteristics was examined collectively and individually for nine metropolitan areas of the United States?Portland, Oregon; Salt Lake City, Utah; Denver, Colorado; Dallas?Forth Worth, Texas; Milwaukee?Green Bay, Wisconsin; Birmingham, Alabama; Atlanta, Georgia; Raleigh, North Carolina; and Boston, Massachusetts. The study was part of a larger study conducted by the U.S. Geological Survey from 1999 to 2004 to examine the effects of urbanization on the physical, chemical, and biological components of stream ecosystems. The objectives of the current study were to determine how stream habitat and geomorphic characteristics relate to different aspects of urbanization across a variety of diverse environmental settings and spatial scales. A space-for-time rural-to-urban land-cover gradient approach was used. Reach-scale habitat data and geomorphic characteristic data were collected once during low flow and included indicators of potential habitat degradation such as measures of channel geometry and hydraulics, streambed substrate, low-flow reach volume (an estimate of base-flow conditions), habitat complexity, and riparian/bank conditions. Hydrologic metrics included in the analyses were those expected to be altered by increases in impervious surfaces, such as high-flow frequency and duration, flashiness, and low-flow duration. Other natural and human features, such as reach-scale channel engineering, geologic setting, and slope, were quantified to identify their possible confounding influences on habitat relations with watershed-scale urbanization indicators. Habitat and geomorphic characteristics were compared to several watershed-scale indicators of urbanization, natural landscape characteristics, and hydrologic metrics by use of correlation analyses and stepwise linear regression. Habitat and geomorphic characteristics were related to percentages of impervious surfaces only in some metropolitan areas and environmental settings. The relations between watershed-scale indicators of urbanization and stream habitat depended on physiography and climate, hydrology, pre-urban channel alterations, reach-scale slope and presence of bedrock, and amount of bank stabilization and grade control. Channels increased in size with increasing percentages of impervious surfaces in southeastern and midwestern metropolitan areas regardless of whether the pre-existing land use was forest or agriculture. The amount of enlargement depended on annual precipitation and frequency of high-flow events. The lack of a relation between channel enlargement and increasing impervious surfaces in other metropolitan areas was thought to be confounded by pre-urbanization hydrologic and channel alterations. Direct relations of channel shape and streambed substrate to urbanization were variable or lacking, probably because the type, amount, and source of sediment are dependent on the phase of urbanization. Reach-scale slope also was important for determining variations in streambed substrate and habitat complexity (percentage of riffles and runs). Urbanization-associated changes in reach-scale riparian vegetation varied geographically, partially depending on pre-existing riparian vegetation characteristics. Bank erosion increased in Milwaukee?Green Bay and Boston urban streams, and bank erosion also increased with an increase in a streamflow flashiness index. However, potential relations likely were confounded by the frequent use of channel stabilization and bank protection in urban settings. Low-flow reach volume did not decrease with increasing urbanization, but instead was related to natural landscape characteristics and possibly other unmeasured factors. The presence of intermittent bedrock in some sampled reaches likely limited some geomorphic responses to urbanization, such as channel bed erosion. Results from this study emphasize the importance of including a wide range of landscape variables at m

Scientific Investigations Report

Sources and characteristics of dissolved organic carbon in the McKenzie River, Oregon, related to the formation of disinfection by-products in treated drinking water

Executive Summary This study characterized the concentration and quality of dissolved organic carbon (DOC) in the McKenzie River, a relatively undeveloped watershed in western Oregon, and its link to forming disinfection by-products (DBPs) in treated drinking water. The study aimed to identify the primary source(s) of DOC in source water for the Eugene Water & Electric Board’s (EWEB) conventional treatment plant on the McKenzie River near river mile 11, upstream of Hayden Bridge. The two classes of regulated compounds examined—trihalomethanes (THMs) and haloacetic acids (HAAs)—form when organic carbon in raw source water reacts with chlorine and (or) bromine during water treatment. The objectives of the study were to: characterize the amount and quality of DOC in the McKenzie River and select tributaries during storms; identify the most common types of carbon using UV-vis spectroscopy and other methods; evaluate optical properties for predicting DBP precursors in surface water; and identify land cover classes or vegetation types that may be important sources of organic carbon and DBP precursors in EWEB’s source water. Eleven storms were sampled synoptically in upstream-to-downstream fashion to provide a “snapshot” of water quality conditions at four sites on the McKenzie River from Frissell Bridge (6 miles downstream from Trail Bridge Reservoir) to the EWEB water treatment plant at Hayden Bridge and nine contributing tributaries. Storms included late summer and early autumn “first flush” events and late autumn, winter, and spring storms spanning a range in streamflows from 3,000 to 26,000 cubic feet per second as measured in the main stem McKenzie River at the EWEB water intake. Water samples were analyzed for DOC concentrations and optical properties (fluorescence and ultraviolet absorbance [UVA]) across a range of wavelengths to characterize the quantity and quality of dissolved organic matter (DOM) in the McKenzie River at the drinking water intake and upstream locations. Paired sets of source and finished water samples were collected at the EWEB treatment plant to identify DOC quality parameters in raw source water that might predict DBP concentrations in finished drinking water. DOC concentrations were relatively low in the McKenzie River (0.4–3 milligrams per liter [mg/L]; average 1.5 mg/L) but much higher in the tributaries. The highest DOC concentrations occurred during “first flush” storms in October 2012 and September 2013; the highest value (16 mg/L) was measured at the 52nd Street stormwater outfall. The average DOC concentration in the lower basin-tributaries was 3.8 mg/L; three middle basin tributaries—Quartz, Gate, and Haagen Creeks, which drain private forestland with less coniferous forest compared with other higher elevation tributaries— had slightly lower average DOC concentrations (2.8 mg/L). These middle-basin watersheds may be important sources of DOC and DBP precursors to the McKenzie River, even more so than the lower basin tributaries, depending on their flows (and loads). This is particularly true after the September 2020 Holiday Farm fire, which burned much of this area. DOC concentrations increased 68 percent in the McKenzie River between the uppermost reference site at Frissell Bridge and Vida; this includes drainage from Quartz Creek, Blue River Lake and Cougar Reservoir, which all contributed DOC to the main stem. In contrast, the lowermost tributaries draining most of the agricultural and urban land did not have a large effect on DOC in the McKenzie River despite their higher DOC concentrations because of their presumed relatively low streamflows and, consequently, DOC loads. Apart from the continuous flow monitors in the McKenzie River and some tributaries (Blue River and South Fork McKenzie River, and streamflow at Hayden Bridge and Vida, Camp Creek and some other locations), streamflow was not assessed during sample collection for this study. This lack of streamflow data precludes a detailed analysis of loads, which is discussed in the future studies section. All DBP concentrations in finished drinking water were less than EPA maximum contaminant levels (MCLs) of 0.080 mg/L for the four trihalomethanes (THM4) and 0.060 mg/L for five haloacetic acids (HAA5). During the 11 storm sampling events the maximum summed concentrations were about 0.040 mg/L for both THM4 and HAA5. Compliance monitoring samples, collected separately by EWEB, yielded some higher concentrations—0.046 mg/L THM4 and 0.047 HAA5—during the December 2012 storm. The corresponding benchmark quotient (BQ) values, which indicate how close a measured DBP concentration is to the MCL, were 0.58 and 0.78, respectively, for THM4 and HAA5. Compared with a similar 2007–08 McKenzie River study that did not target storm events, concentrations of THM4 and HAA5 in finished water were 68 percent and 33 percent higher, respectively, during the current study. Due to the high dilution rates in the McKenzie River main stem, many of the individual fluorescence excitation-emission measurements were low (<0.1 Raman units) and approached analytical detection limits. Parallel factor analysis (PARAFAC) resulted in a five-component model (C1–C5) that represents five unique organic fluorophores. Components C1, C2, and C3 represent DOM associated with soil-derived, humic-like, more degraded organic matter. In contrast, components C4 and C5 represent “fresher” DOM, derived from terrestrial and aquatic plants, including algae and cyanobacteria that are common in the McKenzie River and its tributaries and reservoirs. The fluorescence data and PARAFAC modeling suggest that most of the DOC in the McKenzie River originated from terrestrial sources (primarily components C1 and C2). The largest increases in DOC in the main stem occurred in the reach upstream of Vida, from inflows by Quartz Creek, Blue River, South Fork McKenzie River, and other tributaries. Concentrations of DBPs in EWEB’s finished drinking water were positively correlated with DOC concentrations in raw source water (THM4, p <0.05; HAA5, p <0.01) for paired samples collected 12−24 hours apart. DOC concentrations were significantly positively correlated ( p <0.001) with laboratory-based fluorescent dissolved organic matter (fDOM) measurements, suggesting fDOM as a useful parameter for monitoring and predicting DOC concentration in surface water and DBP concentrations in finished water. Of all the PARAFAC components in surface water, C5 had the highest correlations with DBPs in finished water (rho = 0.77–0.84, p <0.01), followed by components C1 and C2 (rho = 0.75 and 0.71, respectively, p <0.01). This C5 carbon is associated with recently produced DOM, possibly from decomposed terrestrial and aquatic vegetation. Model loadings of these three components were considerably higher in the sampled tributaries relative to the main stem McKenzie River, with most of the observed increases in the main stem apparent at Vida. This points to Quartz Creek or other tributaries in the reach between Frissell Bridge and the sampling site near Vida (South Fork McKenzie and Blue Rivers) as potentially key contributors of DOM source material that leads to the production of DBPs in treated drinking water. A limited load analysis showed that the reservoirs contributed 8–37 percent of the instantaneous DOC loads observed at Vida at the time of sampling, which suggests other sources such as Quartz Creek and other streams in the reach between Frissell Bridge and Vida are more important. Random forest analyses identified PARAFAC components C1 and C5 and fluorescence peaks A, C, M, T and N as the best predictors for HAA5 concentrations in finished drinking water, explaining 62.5 percent of the variation. The best predictors for THM4 were C1, C4 + C5, and peaks T, A, and N, which explained 33 percent of the variation. Several land cover and vegetation classes were correlated with DOC concentration and other optical measurements. The percentage of evergreen forest in each of the subwatersheds sampled was negatively correlated ( p <0.001) with DOC concentration and many optical indicators of DOM quantity: UVA 254 , fDOM, and all of the fluorescence peaks. In contrast, mixed (deciduous) forest was positively correlated ( p <0.001) with DOC, fDOM, UVA 254 , and several fluorescence peaks, demonstrating the importance of deciduous leaf fall in generating DOC and DBP precursors. The high level of human activities in the middle and lower portion of the basin—including timber harvesting and road construction on private forestland, agricultural, rural, industrial, and urban development—have resulted in the greatest loss in native coniferous and mixed deciduous forests in the basin. DOC loading from these tributaries and reservoir releases, which contain DOC from terrestrial and aquatic productivity, both enrich the McKenzie River. Concentrations of DOC increased an average of 71 percent (range 30–120 percent) in the McKenzie River between Frissell Bridge, the upstream reference site, and Vida. PARAFAC components C1, C2, and C5—which were correlated with DBPs in finished water—increased, on average, 109–136 percent (range 20–250 percent) in this same Frissell-to-Vida reach. These increases occur from input of tributaries in the middle basin such as Quartz Creek and others, as noted above. Future monitoring, field, and lab studies can improve our understanding of seasonal and spatial sources of organic carbon contributing DBP precursors to the McKenzie River and allow detection of long-term trends resulting from the recent Holiday Farm Fire, which burned 173,393 acres of forestland, including riparian areas along the main stem, and numerous structures, homes, and outbuildings in September 2020. Future studies could examine DOC fluxes and flushing of carbon from the watershed, investigate the role of precipitation amount and intensity in mobilizing carbon and sediment, and evaluate impacts to aquatic communities and human health as part of a post-fire assessment. Other areas ripe for study include evaluating the impacts of potential temperature increases on carbon sequestration and decomposition in the burned and unburned forests and identifying practices that foster sequestration of carbon in forest soils. The use of fluorescence sensors such as fDOM to monitor the concentration and composition of raw water supplies may be improved for detection of specific DBP precursors, to provide continuous and real-time information to treatment plant operators. Future studies that monitor DOM amount and quality, and DBP Formation Potential (FP), particularly during storm events, paired with streamflow measurements, as suggested above, could help identify areas that contribute high DOC loads and thus help managers identify the key areas to focus restoration activities. Other studies could examine treatment options for currently regulated DBPs and potentially unregulated compounds, including advanced biological treatments for their removal. This study was a collaboration between the U.S. Geological Survey (USGS) and EWEB in Eugene, Oregon, with additional funding provided from USGS Cooperative Matching Funds Program.

Oregon

A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations

Managers faced with decisions on threatened and endangered wildlife populations often are lacking detailed information about the species of concern. Integration of genetic applications will provide management teams with a better ability to assess and monitor recovery efforts on imperiled species. The field of molecular biology continues to progress rapidly and many tools are currently available. Presently, little guidance is available to assist researchers and managers with the appropriate selection of genetic tools to study the status of wild manatee populations. We discuss several genetic tools currently employed in the application of conservation genetics, and address the utility of using these tools to determine population status to aid in conservation efforts. As an example, special emphasis is focused on the endangered West Indian manatee (Order Sirenia). All four extant species of sirenians are imperiled throughout their range, predominately due to anthropogenic sources; therefore, the need for genetic information on their population status is direly needed.

Journal of Marine Animals and Their Ecology

Multicriteria decisions and portfolio analysis: Land acquisition for biological and social objectives

Resource allocation for land acquisition is a common multi-objective problem that involves complex trade-offs. The National Wildlife Refuge System (NWRS) of the U.S. Fish and Wildlife Service currently uses the Targeted Resource Acquisition Comparison Tool (TRACT) to allocate funds from the Migratory Bird Conservation Fund (MBCF; established through the Migratory Bird Hunting and Conservation Act of 1934) for land acquisition based on cost-benefit analysis, regional priority rankings of candidate land parcels available for acquisition, and the overall biological contribution to duck population objectives. However, current policy encourages decision makers to consider societal and economic benefits of lands acquired, in addition to their biological benefits to waterfowl. These decisions about portfolio elements (i.e. individual land parcels) require an analysis of the difficult trade-offs among multiple objectives. In the last decade the application of multi-criteria decision analysis (MCDA) methods has been instrumental in aiding decision makers with complex multi-objective decisions. In this study, we present an alternative approach to developing land acquisition portfolios using MCDA and Modern Portfolio Theory (MPT). We describe the development of a portfolio decision analysis tool using constrained optimization for land acquisition decisions by the NWRS. We outline the decision framework, describe development of the prototype tool in Microsoft Excel, and test the results of the tool using land parcels submitted as candidates for MBCF funding in 2019. Our results indicate that the constrained optimization outperformed the traditional TRACT method and ad hoc portfolios developed using current NWRS criteria.

Ecological Applications

Preliminary results from a shallow water benthic grazing study

The nutrient-rich, shallow waters of San Francisco Bay support high rates of primary production, limited not by nutrients but by light availability and benthic grazing (Alpine and others 1992; Cloern 1982). Phytoplankton blooms are an important food source for upper trophic levels. Consequently animal populations, such as fish, may suffer under conditions of high benthic bivalve grazing. It has been hypothesized that several species of fish are suffering as a result of severe decreases in available phytoplankton since the introduction of Potamocorbula amurensis into San Francisco Bay (Feyrer 2003). The extent of reduction in phytoplankton biomass by benthic bivalves is dependent on both physical and biological factors in addition to their spatial and temporal variability. Physical factors identified as important include: (1) vertical mixing rates, which are a function of wind velocity, currents, and bottom roughness; (2) suspended sediment concentrations; and (3) phytoplankton settling rates. The biological factors controlling the extent of phytoplankton grazing include animal density and organism size, pumping rate, food type and concentration, metabolic demands, assimilation efficiency, and behaviour (Wildish and Kristmanson 1997). Several laboratory studies involving model and live clams have shown that benthic grazers can deplete phytoplankton in the water column (for example, Cole and others 1992). Initially, these studies assumed that the water column remained well mixed above benthic suspension feeders; therefore, parameters measured in the bulk water column were believed to be representative of available particle concentration. For this reason many relationships describing the influence of the bulk flow and bulk seston concentration on benthic grazers physiological processes exist (for example, Levinton 1991). Laboratory measurements using live animals have shown that filtration rates vary with free stream velocity (for example, Levinton 1991). Increases in current speed lead to an increase in filtration rate; however, several studies have shown that filtration may cease at some critical current speed. It has been suggested that resuspension, occurring as a result of high current speeds, may be a factor that negatively affects uptake (Cloern 1987; Levinton 1991). Several mechanisms have been invoked to explain the effects of low speed on growth rates of active suspension feeders. These mechanisms include the formation of a concentration boundary layer and the limiting horizontal flux of seston. It is now accepted that a combination of these factors dictates the growth success of benthic grazers in a particular area. Several field studies have shown that concentration boundary layers can form over benthic ecosystems (for example, Frechette and others 1989, Dolmer 2000); however, many of these studies have failed to measure the hydrodynamics needed to calculate benthic grazing rates. Furthermore, calculating benthic grazing rates with vertical measurements at a single point is problematic due to lack of knowledge of the horizontal gradients in seston (Thompson and others, forthcoming). Despite great improvements in our knowledge on the effects of benthic grazers on seston concentrations in water columns, the effects of different hydrodynamic conditions on grazing rates has not been formulated. This makes it difficult to assess the system-wide effect of the benthic ecosystem on phytoplankton concentrations. Furthermore, it affects our ability to predict the potential success of a benthic species, such as the invasive clams Corbicula fluminea and Potamocorbula amurensis. This paper presents the preliminary results of a control volume approach to elucidate the effect of different hydrodynamic conditions on the grazing rates of Corbicula fluminea.

California

Freshwater and saline loads of dissolved inorganic nitrogen to Hood Canal and Lynch Cove, western Washington

Hood Canal is a long (110 kilometers), deep (175 meters) and narrow (2 to 4 kilometers wide) fjord of Puget Sound in western Washington. The stratification of a less dense, fresh upper layer of the water column causes the cold, saltier lower layer of the water column to be isolated from the atmosphere in the late summer and autumn, which limits reaeration of the lower layer. In the upper layer of Hood Canal, the production of organic matter that settles and consumes dissolved oxygen in the lower layer appears to be limited by the load of dissolved inorganic nitrogen (DIN): nitrate, nitrite, and ammonia. Freshwater and saline loads of DIN to Hood Canal were estimated from available historical data. The freshwater load of DIN to the upper layer of Hood Canal, which could be taken up by phytoplankton, came mostly from surface and ground water from subbasins, which accounts for 92 percent of total load of DIN to the upper layer of Hood Canal. Although DIN in rain falling on land surfaces amounts to about one-half of the DIN entering Hood Canal from subbasins, rain falling directly on the surface of marine waters contributed only 4 percent of the load to the upper layer. Point-source discharges and subsurface flow from shallow shoreline septic systems contributed less than 4 percent of the DIN load to the upper layer. DIN in saline water flowing over the sill into Hood Canal from Admiralty Inlet was at least 17 times the total load to the upper layer of Hood Canal. In September and October 2004, field data were collected to estimate DIN loads to Lynch Cove - the most inland marine waters of Hood Canal that routinely contain low dissolved-oxygen waters. Based on measured streamflow and DIN concentrations, surface discharge was estimated to have contributed about one-fourth of DIN loads to the upper layer of Lynch Cove. Ground-water flow from subbasins was estimated to have contributed about one-half of total DIN loads to the upper layer. In autumn 2004, the relative contribution of DIN from shallow shoreline septic systems to the upper layer was higher in Lynch Cove (23 percent) than in the entire Hood Canal. Net transport of DIN into Lynch Cove by marine currents was measured during August and October 2004-a time of high biological productivity. The net transport of lower-layer water into Lynch Cove was significantly diminished relative to the flow entering Hood Canal at its entrance. Even though the net transport of saline water into the lower layer of Lynch Cove was only 119 cubic meters per second, estuarine currents between 33 and 47 m were estimated to have carried more than 35 times the total freshwater load of DIN to the upper layer from surface and ground water, shallow shoreline septic systems, and direct atmospheric rainfall. The subsurface maximums in measured turbidity, chlorophyll a, particulate organic carbon, and particulate organic nitrogen strongly suggest that the upward mixing of nitrate-rich deeper water is a limiting factor in supplying DIN to the upper layer that enhances marine productivity in Lynch Cove. The presence of phosphate in the upper layer in the absence of dissolved inorganic nitrogen also suggests that the biological productivity that leads to low dissolved-oxygen concentrations in the lower layer of Lynch Cove is limited by the supply of nitrogen rather than by phosphate loads. Although the near-shore zones of the shallow parts of Lynch Cove were sampled, a biogeochemical signal from terrestrial nitrogen was not found. Reversals in the normal estuarine circulation suggest that if the relative importance of the DIN load of freshwater terrestrial and atmospheric sources and the DIN load from transport of saline water by the estuarine circulation in controlling dissolved-oxygen concentrations in Lynch Cove is to be better understood, then the physical forces driving Hood Canal circulation must be better defined.

Scientific Investigations Report

California State Waters Map Series — Offshore of Bodega Head, California

Introduction In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California&rsquo;s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology. The Offshore of Bodega Head map area is located in northern California, about 70 km north of San Francisco and about 80 km south of Point Arena. The onshore part of the map area is largely undeveloped, used primarily for recreation, farms and ranches, and a few wineries. The small town of Bodega Bay, located on the east side of Bodega Harbor, is the largest cultural center. Bodega Harbor is an important commercial fishing base and, in season, an active sport fishing and recreation harbor. Much of the coastline from Bodega Head north to about 6 km north of the Russian River is part of Sonoma Coast State Park. The Offshore of Bodega Head map area includes two California Marine Protected Areas, the Bodega Head State Marine Reserve and the northern part of the Bodega Head State Marine Conservation Area. Additionally, the inland parts of two large estuaries in the map area, Estero Americano and Estero de San Antonio, have been designated as State Marine Recreational Management Areas. The map area is cut by the northwest-striking San Andreas Fault, the right-lateral transform boundary between the North American and Pacific plates. This fault juxtaposes rocks of the Jurassic and Cretaceous Franciscan Complex on the northeast with Cretaceous granitic rocks on the southwest, and it has an estimated slip rate of about 17 to 25 mm/yr in this area. The devastating great 1906 California earthquake (M7.8) is thought to have nucleated on the San Andreas Fault offshore of San Francisco, about 80 km south of Bodega Head, with the rupture extending northward through the Offshore of Bodega Head map area and an additional 220 km to the south flank of Cape Mendocino. North of the mouth of Salmon Creek, the coast and shoreline are rugged and scenic, characterized by flights of uplifted marine terraces, rocky promontories, nearshore sea stacks, kelp-rich coves, and both pocket beaches and longer beach strands, the latter of which include Wrights Beach and Portuguese Beach. The coast has lower relief between the mouth of Salmon Creek and Mussel Point, where South Salmon Creek Beach is backed by a large (about 4 km 2 ) complex of coastal sand dunes. The enormous volume of sand on the beach and in the dune field is derived by southward littoral drift from the Russian River, Salmon Creek, and smaller coastal watersheds. The sediment is trapped by protruding bedrock at Mussel Point, which represents the south end of the Russian River littoral cell. Bodega Head is underlain by Cretaceous granitic rocks, and its shoreline is variously characterized by relatively low-lying terraces, steep and high bluffs, and a few pocket beaches. East of Bodega Head, Doran Beach (part of Doran Regional Park) is a 1.7-km-long sand spit that forms the north boundary of Bodega Bay and the south boundary of Bodega Harbor. The coast south of Doran Beach on the east flank of Bodega Bay is composed of rocky bluffs, hummocky marine terraces, and a few small pocket beaches. The bluffs are underlain by sheared rocks of the Franciscan Complex and are highly susceptible to landslides. This section of coast includes two prominent watersheds, Estero Americano and Estero de San Antonio, which drain westward into Bodega Bay. The offshore part of the Offshore of Bodega Head map area is characterized by an extensive, rugged and rocky shelf underlain by Cretaceous granitic rocks. This rocky terrain, centered offshore of Bodega Head, extends northwestward for about 15 km, from the south edge of the map area (where it forms the west boundary of Bodega Bay) to the northern-central part of the map area offshore of the mouth of Salmon Creek. This rocky seafloor reaches water depths of 40 to 80 m and is overlain by young sediment. Circulation over the shelf and seafloor in the map area (and in the broader central California region) is dominated by the southward-flowing California Current, the eastern boundary current of the North Pacific Gyre. Associated upwelling brings cool, nutrient-rich waters to the surface, resulting in high biological productivity. Persistent northwest winds are sometimes weak or absent during the fall and winter, causing the California Current to move farther offshore so that the shelf is affected by the Davidson Current, a weaker northward-flowing countercurrent. As a result, net flow over the continental shelf is commonly southeastward during the spring and summer and northwestward during the fall and winter. Throughout the year, this part of the northern California coast is exposed to four wave climate regimes: the north Pacific swell, the southern swell, northwest wind waves, and local wind waves. The north Pacific swell dominates in winter months (typically November through March). During summer months, the largest waves come from the southern swell, generated by storms in the south Pacific and offshore of Central America. Northwest wind waves affect the coast throughout the year, whereas local wind waves are most common from October to April. Potential marine benthic habitats in the Offshore of Bodega Head map area include unconsolidated continental-shelf sediments, mixed continental-shelf substrate, and hard continental-shelf substrate. Rocky-shelf outcrops and rubble are considered to be promising potential habitats for rockfish and lingcod, both of which are recreationally and commercially important species.

California

Evaluation of reproductive status in Atlantic Tripletail by traditional and nonlethal approaches

Reproductive biology information is an important tool for fishery management actions such as the identification of spawning areas and the development of protective size limits, bag limits, and seasons. Such information for the management of Atlantic Tripletail Lobotes surinamensis is currently limited, particularly in the western Atlantic Ocean, as information regarding the reproductive biology of this species is sparse in the published literature. To this end, we determined the reproductive status of tripletail and compared the results of a nonlethal sampling method, plasma vitellogenin (VTG) analysis, with those of two traditional (lethal) methods, gonadosomatic index (GSI) and gonad histology. A total of 223 (122 male and 101 female) tripletail were sampled over 2 years near Jekyll Island, Georgia. Gonad histology indicated that 107 (94%) of the male tripletail were in the spawning-capable reproductive phase. Female tripletail were found in all reproductive phases, but only nine (8.9%) were in the spawning-capable phase. Plasma VTG was strongly related to GSI in females ( R 2 = 0.832, n = 77), and female GSI differed significantly among reproductive phases ( p < 0.0001). The estimated length at which 50% (L50) of female tripletail reached maturity was 463 mm; however, the L50 for male tripletail could not be determined because of the lack of immature fish within the study sample. Our study provides valuable information for the management of tripletail and indicates that a nonlethal approach (plasma VTG) may be useful for differentiating developing and spawning-capable females from males and from females in other reproductive phases.

Georgia

Estimating suspended solids concentrations from backscatter intensity measured by acoustic Doppler current profiler in San Francisco Bay, California

The estimation of mass concentration of suspended solids is one of the properties needed to understand the characteristics of sediment transport in bays and estuaries. However, useful measurements or estimates of this property are often problematic when employing the usual methods of determination from collected water samples or optical sensors. Analysis of water samples tends to undersample the highly variable character of suspended solids, and optical sensors often become useless from biological fouling in highly productive regions. Acoustic sensors, such as acoustic Doppler current profilers that are now routinely used to measure water velocity, have been shown to hold promise as a means of quantitatively estimating suspended solids from acoustic backscatter intensity, a parameter used in velocity measurement. To further evaluate application of this technique using commercially available instruments, profiles of suspended solids concentrations are estimated from acoustic backscatter intensity recorded by 1200- and 2400-kHz broadband acoustic Doppler current profilers located at two sites in San Francisco Bay, California. ADCP backscatter intensity is calibrated using optical backscatterance data from an instrument located at a depth close to the ADCP transducers. In addition to losses from spherical spreading and water absorption, calculations of acoustic transmission losses account for attenuation from suspended sediment and correction for nonspherical spreading in the near field of the acoustic transducer. Acoustic estimates of suspended solids consisting of cohesive and noncohesive sediments are found to agree within about 8-10% (of the total range of concentration) to those values estimated by a second optical backscatterance sensor located at a depth further from the ADCP transducers. The success of this approach using commercially available Doppler profilers provides promise that this technique might be appropriate and useful under certain conditions in spite of some theoretical limitations of the method. ?? 2004 Elsevier B.V. All rights reserved.

Marine Geology