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Tidal saltmarsh fragmentation and persistence of San Pablo Song Sparrows (Melospiza melodia samuelis): Assessing benefits of wetland restoration in San Francisco Bay

The San Pablo Song Sparrow (Melospiza melodia samuelis) is one of three morphologically distinct Song Sparrow subspecies in tidal marshes of the San Francisco Bay estuary. These subspecies are rare, because as the human population has grown, diking and development have resulted in loss of 79% of the historic tidal marshes. Hundreds of projects have been proposed in the past decade to restore tidal marshes and benefit endemic populations. To evaluate the value of these restoration projects for Song Sparrows, we developed a population viability analysis (PVA) model to examine persistence of samuelis subspecies in relation to parcel size, connectivity, and catastrophe in San Pablo Bay. A total of 101 wetland parcels were identified from coverages of modern and historic tidal marshes. Parcels were grouped into eight fragments in the historical landscape and 10 in the present landscape. Fragments were defined as a group of parcels separated by >1 km, a distance that precluded regular interchange. Simulations indicated that the historic (circa 1850) samuelis population was three times larger than the modern population. However, only very high levels (>70% mortality) of catastrophe would threaten their persistence. Persistence of populations was sensitive to parcel size at a carrying capacity of <10 pairs, but connectivity of parcels was found to have little importance because habitats were dominated by a few large parcels. Our analysis indicates little risk of extinction of the samuelis subspecies with the current extent of tidal marshes, but the vulnerability of the small-est parcels suggests that restoration should create larger continuous tracts. Thus, PVA models may be useful tools for balancing the costs and benefits of restoring habitats for threatened tidal-marsh populations in wetland restoration planning.

Studies in Avian Biology

Enhanced surveillance strategies for detecting and monitoring chronic wasting disease in free-ranging cervids

The purpose of this document is to provide wildlife management agencies with the foundation upon which they can build scientifically rigorous and cost-effective surveillance and monitoring programs for chronic wasting disease (CWD) or refine their existing programs. The first chapter provides an overview of potential demographic and spatial risk factors of susceptible wildlife populations that may be exploited for CWD surveillance and monitoring. The information contained in this chapter explores historic as well as recent developments in our understanding of CWD disease dynamics. It also contains many literature references for readers who may desire a more thorough review of the topics or CWD in general. The second chapter examines methods for enhancing efforts to detect CWD on the landscape where it is not presently known to exist and focuses on the efficiency and cost-effectiveness of the surveillance program. Specifically, it describes the means of exploiting current knowledge of demographic and spatial risk factors, as described in the first chapter, through a two-stage surveillance scheme that utilizes traditional design-based sampling approaches and novel statistical methods to incorporate information about the attributes of the landscape, environment, populations and individual animals into CWD surveillance activities. By accounting for these attributes, efficiencies can be gained and cost-savings can be realized. The final chapter is unique in relation to the first two chapters. Its focus is on designing programs to monitor CWD once it is discovered within a jurisdiction. Unlike the prior chapters that are more detailed or prescriptive, this chapter by design is considerably more general because providing comprehensive direction for creating monitoring programs for jurisdictions without consideration of their monitoring goals, sociopolitical constraints, or their biological systems, is not possible. Therefore, the authors draw upon their collective experiences implementing disease-monitoring programs to present the important questions to consider, potential tools, and various strategies for those wildlife management agencies endeavoring to create or maintain a CWD monitoring program. Its intent is to aid readers in creating efficient and cost-effective monitoring programs, while avoiding potential pitfalls. It is hoped that these three chapters will be useful tools for wildlife managers struggling to implement efficient and effective CWD disease management programs.

Open-File Report

Trends in Rocky Mountain amphibians and the role of beaver as a keystone species

Despite prevalent awareness of global amphibian declines, there is still little information on trends for many widespread species. To inform land managers of trends on protected landscapes and identify potential conservation strategies, we collected occurrence data for five wetland-breeding amphibian species in four national parks in the U.S. Rocky Mountains during 2002&ndash;2011. We used explicit dynamics models to estimate variation in annual occupancy, extinction, and colonization of wetlands according to summer drought and several biophysical characteristics (e.g., wetland size, elevation), including the influence of North American beaver ( Castor canadensis ). We found more declines in occupancy than increases, especially in Yellowstone and Grand Teton national parks (NP), where three of four species declined since 2002. However, most species in Rocky Mountain NP were too rare to include in our analysis, which likely reflects significant historical declines. Although beaver were uncommon, their creation or modification of wetlands was associated with higher colonization rates for 4 of 5 amphibian species, producing a 34% increase in occupancy in beaver-influenced wetlands compared to wetlands without beaver influence. Also, colonization rates and occupancy of boreal toads ( Anaxyrus boreas ) and Columbia spotted frogs ( Rana luteiventris ) were ⩾2 times higher in beaver-influenced wetlands. These strong relationships suggest management for beaver that fosters amphibian recovery could counter declines in some areas. Our data reinforce reports of widespread declines of formerly and currently common species, even in areas assumed to be protected from most forms of human disturbance, and demonstrate the close ecological association between beaver and wetland-dependent species.

Biological Conservation

Designing ecological climate change impact assessments to reflect key climatic drivers

Identifying the climatic drivers of an ecological system is a key step in assessing its vulnerability to climate change. The climatic dimensions to which a species or system is most sensitive – such as means or extremes – can guide methodological decisions for projections of ecological impacts and vulnerabilities. However, scientific workflows for combining climate projections with ecological models have received little explicit attention. We review Global Climate Model (GCM) performance along different dimensions of change and compare frameworks for integrating GCM output into ecological models. In systems sensitive to climatological means, it is straightforward to base ecological impact assessments on mean projected changes from several GCMs. Ecological systems sensitive to climatic extremes may benefit from what we term the ‘model space’ approach: a comparison of ecological projections based on simulated climate from historical and future time periods. This approach leverages the experimental framework used in climate modeling, in which historical climate simulations serve as controls for future projections. Moreover, it can capture projected changes in the intensity and frequency of climatic extremes, rather than assuming that future means will determine future extremes. Given the recent emphasis on the ecological impacts of climatic extremes, the strategies we describe will be applicable across species and systems. We also highlight practical considerations for the selection of climate models and data products, emphasizing that the spatial resolution of the climate change signal is generally coarser than the grid cell size of downscaled climate model output. Our review illustrates how an understanding of how climate model outputs are derived and downscaled can improve the selection and application of climatic data used in ecological modeling.

Global Change Biology

Multiscale thermal refugia and stream habitat associations of chinook salmon in northwestern Oregon

We quantified distribution and behavior of adult spring chinook salmon ( Oncorhynchus tshawytscha ) related to patterns of stream temperature and physical habitat at channel-unit, reach-, and section-level spatial scales in a wilderness stream and a disturbed stream in the John Day River basin in northeastern Oregon. We investigated the effectiveness of thermal remote sensing for analyzing spatial patterns of stream temperature and assessed habitat selection by spring chinook salmon, evaluating whether thermal refugia might be responsible for the persistence of these stocks in rivers where water temperatures frequently exceed their upper tolerance levels (25°C) during spawning migration. By presenting stream temperature and the ecology of chinook salmon in a historical context, we could evaluate how changes in riverine habitat and thermal spatial structure, which can be caused by land-use practices, may influence distributional patterns of chinook salmon. Thermal remote sensing provided spatially continuous maps of stream temperature for reaches used by chinook salmon in the upper subbasins of the Middle Fork and North Fork John Day River. Electivity analysis and logistic regression were used to test for associations between the longitudinal distribution of salmon and cool-water areas and stream habitat characteristics. Chinook salmon were distributed nonuniformly in reaches throughout each stream. Salmon distribution and cool water temperature patterns were most strongly related at reach-level spatial scales in the warm stream, the Middle Fork (maximum likelihood ratio: P < 0.01), and most weakly related in the cold stream, the North Fork ( P > 0.30). Pools were preferred by adult chinook salmon in both subbasins (Bonferroni confidence interval: P ≤ 0.05); however, riffles were used proportionately more frequently in the North Fork than in the Middle Fork. Our observations of thermal refugia and their use by chinook salmon at multiple spatial scales reveal that, although heterogeneity in the longitudinal stream temperature profile may be viewed as an ecological warning sign, thermal patchiness in streams also should be recognized for its biological potential to provide habitat for species existing at the margin of their environmental tolerances.

Oregon

Changes in growth of Rainbow Trout in a Catskill Mountain Reservoir following Alewife and White Perch Introductions

Rainbow Trout Oncorhynchus mykiss were introduced to the Esopus Creek watershed in the Catskill Mountains of New York in the early 1880s. This introduction created a renowned naturalized fishery that remains important to the local economy today. The objective of this study was to determine whether the growth and condition of Rainbow Trout in the Ashokan Reservoir changed following the establishment of (1) Alewives Alosa pseudoharengus in the 1970s and (2) White Perch Morone americana in the 2000s by analyzing historical scale samples from 502 Rainbow Trout. The resulting data were used to compare length at age, von Bertalanffy growth curves, age‐specific annual growth increments, and relative weight before and after each introduction. Results indicated that growth of Rainbow Trout of ages <5 years generally increased following each introduction, while insufficient data for ages 5 and 6 made trends for older fish unclear. Rainbow Trout of ages ≤2 are believed to primarily use riverine habitats in this watershed, and therefore fish of ages >2 may best reflect reservoir growth. The mean relative weight of Rainbow Trout also increased between each period. The largest increases in both growth and condition were observed during the period after the introduction of White Perch, which was unexpected considering this species may have some diet overlap with Rainbow Trout and should be a poor forage species. Changes in watershed management and density‐dependent growth effects may explain these unexpected results. Our results, which largely suggest increased growth and condition over time, eliminate growth effects as a possible explanation for declining Rainbow Trout populations and suggest recruitment issues in the watershed require further investigation. This study contributes to our understanding of the interactions between introduced species and underscores the value of maintaining long‐term monitoring programs for assessing biological trends.

New York

Sediment transport in two tributaries to the San Joaquin River immediately below Friant Dam—Cottonwood Creek and Little Dry Creek, California

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow dynamics between October 1, 2011, and September 30, 2019. The two systems deliver sediment to the San Joaquin River below Friant Dam, California. Dams create downstream discontinuities in streamflow and sediment transport and therefore influence fish habitat and sediment dynamics. Because these two creeks are directly downriver from Friant Dam, they become the most upstream source of sediment to the San Joaquin River below Friant Dam. The quality and quantity of spawning habitat for fish in the gravel-bedded reach of the San Joaquin River relies on a range of bed material particle size suitable for redd structure. The effects of coarse-sand to fine-gravel supply on salmonid habitat depends primarily on the size of the sediment and the timing of its addition from tributaries to the San Joaquin River; thus, understanding the timing, quantity, and size of sediment supplied from these two tributaries is critical to the management of ecological and biological sustainability. Streamflow from Cottonwood and Little Dry Creeks, along with streamflow from the San Joaquin River below Friant Dam, were compared to continuously measured water-surface elevations to quantify the timing and direction of streamflow. Suspended-sediment samples were collected with multiple automatic samplers and analyzed for concentration and grain-size distribution. Measured suspended-sediment concentrations and streamflows were used to develop sediment rating curves and compute continuous estimates of suspended-sediment load for each tributary. Satellite imagery was used to qualify spatial and temporal dynamics through the lower watersheds and support more quantitative sediment-load estimates. Computed annual sediment loads ranged from 1.32x10 1 to 2.68x10 4 metric tons for Little Dry Creek and 9.82 to 1.98x10 3 metric tons for Cottonwood Creek. Sediment loads computed during the study period for both watersheds show that annual loads were highest during water year 2017 (October 1, 2016, to September 30, 2017). Sediment transport primarily occurred between the months of January and March. In both tributaries, grain-size distributions of suspended sediment were predominantly coarse-sized sand and were finer than the remnant bed material. Both creeks demonstrate backwater effects from the San Joaquin River, but the more tortuous stream channel and historical mining pits within Little Dry Creek provide more capacity for sediment storage compared to the less complex stream network of Cottonwood Creek. Because loads were computed based on upstream streamgages and not at the confluence of each tributary to the San Joaquin River, annual load estimates do not represent direct flux into the San Joaquin River; instead, these results indicated that in Little Dry Creek, particularly, the lowest portion of the watershed stores sediment before it reaches the San Joaquin River.

California

Climate science and famine early warning

Food security assessment in sub-Saharan Africa requires simultaneous consideration of multiple socio-economic and environmental variables. Early identification of populations at risk enables timely and appropriate action. Since large and widely dispersed populations depend on rainfed agriculture and pastoralism, climate monitoring and forecasting are important inputs to food security analysis. Satellite rainfall estimates (RFE) fill in gaps in station observations, and serve as input to drought index maps and crop water balance models. Gridded rainfall time-series give historical context, and provide a basis for quantitative interpretation of seasonal precipitation forecasts. RFE are also used to characterize flood hazards, in both simple indices and stream flow models. In the future, many African countries are likely to see negative impacts on subsistence agriculture due to the effects of global warming. Increased climate variability is forecast, with more frequent extreme events. Ethiopia requires special attention. Already facing a food security emergency, troubling persistent dryness has been observed in some areas, associated with a positive trend in Indian Ocean sea surface temperatures. Increased African capacity for rainfall observation, forecasting, data management and modelling applications is urgently needed. Managing climate change and increased climate variability require these fundamental technical capacities if creative coping strategies are to be devised.

Philosophical Transactions of the Royal Society B:

Carcass analog provides marine subsidies for macroinvertebrates and juvenile Atlantic 8 salmon in temperate oligotrophic streams

Anadromous fish populations entering freshwater ecosystems provide organic matter and marine-derived nutrients during spawning and subsequent mortalities of adults. Dams and other impediments to connectivity in rivers and streams have affected anadromous fish populations in many regions and prevented or reduced this influx of organic materials and nutrients. This study used historical data on the timing of delivery of marine-derived nutrients; we added a carcass analogue (pellets made from the carcasses of Chinook salmon, Oncorhynchus tschawytcha ) to simulate potential effects of restored access of anadromous fish to streams. We used stable isotopes to document the extent of nutrient incorporation of nitrogen and carbon from the carcass analogue by macroinvertebrates and juvenile Atlantic salmon ( Salmo salar ) in salmon nursery streams. We stocked four headwater streams that historically hosted spawning Atlantic salmon and sea lamprey ( Petromyzon marinus ) in Maine, U.S.A. with Atlantic salmon fry and simulated timing of nutrient addition by spawning sea lamprey in the early summer and Atlantic salmon in the autumn. Macroinvertebrates and Atlantic salmon assimilated nitrogen (12&ndash;57% of total N) and carbon (21&ndash;65% of total C) from the added pellets, and the magnitude and duration of enrichment varied temporally and with macroinvertebrate functional feeding group. Assimilation of nutrients from carcass analogues was both direct and indirect, and a nutrient legacy was evident in the second year of sampling. Incorporation of nutrients from the pellets at a range of heights in the food web demonstrated the potential for marine-derived subsidies to contribute to freshwater ecosystem processes in Atlantic salmon nursery streams.

Freshwater Biology

Metal concentrations in surface sediments of Boston Harbor: Changes with time

The concentrations of metals in surface sediments of Boston Harbor have decreased during the period 1977–1993. This conclusion is supported by analysis of: (1) surface sediments collected at monitoring stations in the outer harbor between 1977 and 1993; (2) metal concentration profiles in sediment cores from depositional areas of the harbor; and (3) historical data from a contaminated-sediment database, which includes information on metal and organic contaminants and sediment texture. The background and matrix-corrected concentrations of lead (Pb) measured in the surficial layer (0–2 cm) of cores decreased by an average of 46%±12% among four locations in the outer harbor during the 16 y period. Chromium (Cr), copper (Cu), mercury (Hg), silver (Ag), and zinc (Zn) exhibited similar trends. Results from our sediment sampling are supported by historical data that were compiled from diverse sources into a regional sediment database. This sediment database contains approximately 3000 samples; of these, about 460 samples were collected and analyzed for Cu, Hg, or Zn and many other sediment parameters in Boston Harbor surface sediments between 1971–1993. The database indicates that the concentrations of these three metals also decreased with time in Boston’s Inner Harbor. The decreases in metal concentrations that are observed in more recent years parallel a general decrease in the flux of metals to the harbor, implemented by: (1) ending the sewage sludge discharge to the Harbor in December, 1991; (2) greater source reduction (e.g. recovery of silver from photographic processing) and closing or moving of industries; (3) improvements in wastewater handling and sewage treatment; and (4) diminishing use of lead in gasoline beginning about 1973. Despite the general decrease in metal concentrations in Boston Harbor surface sediments, the concentrations of Ag and Hg measured at some outer harbor stations in 1993 were still at, or above, the level associated with frequent adverse effects to marine organisms (guidelines are: Ag 3.7 μ g g −1 , Hg 1.17 μ g g −1 , from Long et al., 1995 ). Concentrations of the other metals listed were in the range considered to occasionally induce adverse biological effects.

Massachusetts

Scenarios and strategies for future-proofing ecosystem management under climatic novelty

Climate change is driving unprecedented declines in dominant, habitat-forming foundation species across marine and terrestrial ecosystems globally. As climatic novelty becomes the norm, ecosystem reassembly will become increasingly common. Predicting and understanding these transitions, and their implications for future ecosystem functioning, is essential for designing effective forward-looking management strategies. We explored 3 scenarios that describe a range of ecosystem reassembly trajectories following declines in previously dominant habitat-forming taxa: compensation, in which functionally similar subdominant or immigrating taxa maintain ecosystem structure and function; decline, in which no compensation occurs leading to loss of ecosystem structure and function; and transformation, in which the ecosystem present historically can no longer persist and shifts into a fundamentally different ecosystem type with distinct structure and function. This range of potential outcomes highlights the urgent need to assess the ecological feasibility and functional implications of potential management actions. Scientists and managers can work together to quantify local-scale climatic novelty and ecosystem resilience to better predict the most likely reassembly trajectories and identify management interventions that will optimize ecosystem function. This approach would allow for more proactive planning to support persistence of ecosystem structure and function, helping to future-proof ecosystem management in a rapidly changing world.

Conservation Biology

Simulation of flow and sediment mobility using a multidimensional flow model for the White Sturgeon critical-habitat reach, Kootenai River near Bonners Ferry, Idaho

In 1994, the Kootenai River white sturgeon (Acipenser transmontanus) was listed as an Endangered Species as a direct result of two related observations. First, biologists observed that the white sturgeon population in the Kootenai River was declining. Second, they observed a decline in recruitment of juvenile sturgeon beginning in the 1950s with an almost total absence of recruitment since 1974, following the closure of Libby Dam in 1972. This second observation was attributed to changes in spawning and (or) rearing habitat resulting from alterations in the physical habitat, including flow regime, sediment-transport regime, and bed morphology of the river. The Kootenai River White Sturgeon Recovery Team was established to find and implement ways to improve spawning and rearing habitat used by white sturgeon. They identified the need to develop and apply a multidimensional flow model to certain reaches of the river to quantify physical habitat in a spatially distributed manner. The U.S. Geological Survey has addressed these needs by developing, calibrating, and validating a multidimensional flow model used to simulate streamflow and sediment mobility in the white sturgeon critical-habitat reach of the Kootenai River. This report describes the model and limitations, presents the results of a few simple simulations, and demonstrates how the model can be used to link physical characteristics of streamflow to biological or other habitat data. This study was conducted in cooperation with the Kootenai Tribe of Idaho along a 23-kilometer reach of the Kootenai River, including the white sturgeon spawning reach near Bonners Ferry, Idaho that is about 108 to 131 kilometers below Libby Dam. U.S. Geological Survey's MultiDimensional Surface-Water Modeling System was used to construct a flow model for the critical-habitat reach of the Kootenai River white sturgeon, between river kilometers 228.4 and 245.9. Given streamflow, bed roughness, and downstream water-surface elevation, the model computes the velocity field, water-surface elevations, and boundary shear stress throughout the modeled reach. The 17.5 kilometer model reach was subdivided into two segments on the basis of predominant grain size: a straight reach with a sand, gravel, and cobble substrate located between the upstream model boundary at river kilometer 245.9 and the upstream end of Ambush Rock at river kilometer 244.6, and a meandering reach with a predominately sand substrate located between upstream end of Ambush Rock and the downstream model boundary at river kilometer 228.4. Model cell size in the x and y (horizontal) dimensions is 5 meters by 5 meters along the computational grid centerline with 15 nodes in the z (vertical) dimension. The model was calibrated to historical streamflows evenly distributed between 141.6 and 2,548.9 cubic meters per second. The model was validated by comparing simulated velocities with velocities measured at 15 cross sections during steady streamflow. These 15 cross sections were each measured multiple (7-13) times to obtain velocities suitable for comparison to the model results. Comparison of modeled and measured velocities suggests that the model does a good job of reproducing flow patterns in the river, although some discrepancies were noted. The model was used to simulate water-surface elevation, depth, velocity, bed shear stress, and sediment mobility for Kootenai River streamflows of 170, 566, 1,130, 1,700, and 2,270 cubic meters per second (6,000, 20,000, 40,000, 60,000, and 80,000 cubic feet per second). The three lowest streamflow simulations represent a range of typical river conditions before and since the construction of Libby Dam, and the highest streamflow simulation (2,270 cubic meters per second) is approximately equal to the annual median peak streamflow prior to emplacement of Libby Dam in 1972. Streamflow greater than 566 cubic meters per second were incrementally increased by 570 cubic meters per second. For each

Scientific Investigations Report

An evaluation of effects of groundwater exchange on nearshore habitats and water quality of western Lake Erie

Historically, the high potentiometric surface of groundwater in the Silurian/Devonian carbonate aquifer in Monroe County, MI resulted in discharge of highly mineralized, SO 4 -rich groundwater to the Lake Erie shoreline near both Erie State Game Area (ESGA) and Pointe Mouillee State Game Area (PMSGA). Recently, regional groundwater levels near PMSGA have been drawn down as much as 45 m below lake level in apparent response to quarry dewatering. From August to November of 2003, we conducted preliminary studies of groundwater flow dynamics and chemistry, shallow lake water chemistry, and fish and invertebrate communities at both sites. Consistent with regional observations, groundwater flow direction in the nearshore at ESGA was upward, or toward Lake Erie, and shallow nearshore groundwater chemistry was influenced by regional groundwater chemistry. In contrast, at PMSGA, the groundwater flow potential was downward and lake water, influenced by quarry discharge seeping downward into nearshore sediments, produced a different lake and shallow groundwater chemistry than at ESGA. Although the invertebrate and young fish community was similar at the two sites, taxonomic groups tolerant of degraded water quality were more prevalent at PMSGA. Sensitive taxa were more prevalent at ESGA. We propose a conceptual model, based on well-described models of groundwater/seawater interaction along coastal margins, to describe the interconnection among geologic, hydrologic, chemical, and biological processes in the different nearshore habitats of Lake Erie, and we identify processes that warrant further detailed study in the Great Lakes.

Lake Erie

Environmental threats to tidal-marsh vertebrates of the San Francisco Bay estuary

The San Francisco Bay and delta system comprises the largest estuary along the Pacific Coast of the Americas and the largest remaining area for tidal-marsh vertebrates, yet tidal marshes have been dramatically altered since the middle of the 19th century. Although recent efforts to restore ecological functions are notable, numerous threats to both endemic and widespread marsh organisms, including habitat loss, are still present. The historic extent of wetlands in the estuary included 2,200 km2 of tidal marshes, of which only 21% remain, but these tidal marshes comprise >90% of all remaining tidal marshes in California. In this paper, we present the most prominent environmental threats to tidal-marsh vertebrates including habitat loss (fragmentation, reductions in available sediment, and sea-level rise), habitat deterioration (contaminants, water quality, and human disturbance), and competitive interactions (invasive species, predation, mosquito and other vector control, and disease). We discuss these threats in light of the hundreds of proposed and ongoing projects to restore wetlands in the estuary and suggest research needs to support future decisions on restoration planning.

Studies in Avian Biology

A multiscale natural community and species-level vulnerability assessment of the Gulf Coast, USA

Vulnerability assessments combine quantitative and qualitative evaluations of the exposure, sensitivity, and adaptive capacity of species or natural communities to current and future threats. When combined with the economic, ecological or evolutionary value of the species, vulnerability assessments quantify the relative risk to regional species and natural communities and can enable informed prioritization of conservation efforts. Vulnerability assessments are common practice in conservation biology, including the potential impacts of future climate scenarios. However, geographic variation in scenarios and vulnerabilities is rarely quantified. This gap is particularly limiting for informing ecosystem management given that conservation practices typically vary by sociopolitical boundaries rather than by ecological boundaries. To support prioritization of conservation actions across a range of spatial scales, we conducted the Gulf Coast Vulnerability Assessment (GCVA) for four natural communities and eleven focal species around the Gulf of Mexico based on current and future threats from climate change and land-use practices out to 2060. We used the Standardized Index of Vulnerability and Value (SIVVA) tool to assess both natural community and species vulnerabilities. We observed greater variation across ecologically delineated subregions within the Gulf Coast of the U.S. than across climate scenarios. This novel finding suggests that future vulnerability assessments incorporate regional variation and that conservation prioritization may vary across ecological subregions. Across subregions and climate scenarios the most prominent threats were legacy effects, primarily from habitat loss and degradation, that compromised the adaptive capacity of species and natural communities. The second most important threats were future threats from sea-level rise. Our results suggest that the substantial threats species and natural communities face from climate change and sea-level rise would be within their adaptive capacity were it not for historic habitat loss, fragmentation, and degradation.

Alabama, Florida, Georgia, Louisiana, Mississippi,

Assessment of potential recovery viability for Colorado Pikeminnow Ptychocheilus lucius in the Colorado River in Grand Canyon

Colorado Pikeminnow Ptychocheilus lucius, the Colorado River’s top native predatory fish, was historically distributed from the Gulf of California delta to the upper reaches of the Green, Colorado, and San Juan rivers in the Colorado River basin in the Southwestern US. In recent decades Colorado Pikeminnow population abundance has declined, primarily due to predation by warmwater nonnative fish and habitat modification following dam construction. Small, reproducing populations remain in the Green and upper Colorado rivers, but their current population trajectory is declining and the San Juan River population is maintained primarily through stocking. As such, establishment of an additional population could aid recovery efforts and increase the species’ resilience and population redundancy. The Colorado River in Grand Canyon once supported Colorado Pikeminnow, but until recently habitat suitability in this altered reach was considered low due to a depressed thermal regime and abundant nonnative predators. Climate change and ongoing drought has presented an opportunity to evaluate the feasibility of native fish restoration in a system where declining reservoir storage has led to warmer releases and re-emergence of riverine habitat. These changes in the physical attributes of the river have occurred in concert with a system-wide decline in nonnative predators. Conditions ten years ago were not compatible with reintroduction feasibility in Grand Canyon; however, due to rapidly changing conditions an expert Science Panel was convened to evaluate whether the physical and biological attributes of this reach could now support various life stages of Colorado Pikeminnow. Here, we report on the evaluation process and outcome from the Science Panel, which developed a science-based recommendation to the U.S. Fish and Wildlife Service on reintroduction feasibility. The Science Panel concluded that current habitat attributes in Grand Canyon could satisfy some, but perhaps not all, Colorado Pikeminnow life history requirements. This reach has the potential to support adult and sub-adult growth, foraging, migrations, and spawning, but low juvenile survival may limit recruitment. However, populations of other native species are successfully reproducing and increasing in western Grand Canyon, even in areas once considered suboptimal habitat. Should managers decide to move to the next phase of this process, actions such as experimental stocking and monitoring, telemetry studies, bioenergetics modeling, and laboratory-based research may provide additional information to further evaluate a potential reintroduction effort in this rapidly changing but highly altered system.

Arizona

Genome-wide analysis of SNPs is consistent with no domestic dog ancestry in the endangered Mexican Wolf (Canis lupus baileyi)

The Mexican gray wolf ( Canis lupus baileyi ) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in 3 separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from 3, 2, and 2 founders, respectively. These lineages were merged in 1995 to increase the available genetic variation, and Mexican wolves were reintroduced into Arizona and New Mexico in 1998. Despite the ongoing management of the Mexican wolf population, it has been suggested that a proportion of the Mexican wolf ancestry may be recently derived from hybridization with domestic dogs. In this study, we genotyped 87 Mexican wolves, including individuals from all 3 captive lineages and cross-lineage wolves, for more than 172000 single nucleotide polymorphisms. We identified levels of genetic variation consistent with the pedigree record and effects of genetic rescue. To identify the potential to detect hybridization with domestic dogs, we compared our Mexican wolf genotypes with those from studies of domestic dogs and other gray wolves. The proportion of Mexican wolf ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and was consistent with simulated levels of incomplete lineage sorting. Overall, our results suggested that Mexican wolves lack biologically significant ancestry with dogs and have useful implications for the conservation and management of this endangered wolf subspecies.

Journal of Heredity

Incorporating uncertainty into mercury-offset decisions with a probabilistic network for National Pollutant Discharge Elimination System permit holders: An interim report

This interim report describes an alternative approach for evaluating the efficacy of using mercury (Hg) offsets to improve water quality. Hg-offset programs may allow dischargers facing higher-pollution control costs to meet their regulatory obligations by making more cost effective pollutant-reduction decisions. Efficient Hg management requires methods to translate that science and economics into a regulatory decision framework. This report documents the work in progress by the U.S. Geological Survey’s Western Geographic Science Center in collaboration with Stanford University toward developing this decision framework to help managers, regulators, and other stakeholders decide whether offsets can cost effectively meet the Hg total maximum daily load (TMDL) requirements in the Sacramento River watershed. Two key approaches being considered are: (1) a probabilistic approach that explicitly incorporates scientific uncertainty, cost information, and value judgments; and (2) a quantitative approach that captures uncertainty in testing the feasibility of Hg offsets. Current fate and transport-process models commonly attempt to predict chemical transformations and transport pathways deterministically. However, the physical, chemical, and biologic processes controlling the fate and transport of Hg in aquatic environments are complex and poorly understood. Deterministic models of Hg environmental behavior contain large uncertainties, reflecting this lack of understanding. The uncertainty in these underlying physical processes may produce similarly large uncertainties in the decisionmaking process. However, decisions about control strategies are still being made despite the large uncertainties in current Hg loadings, the relations between total Hg (HgT) loading and methylmercury (MeHg) formation, and the relations between control efforts and Hg content in fish. The research presented here focuses on an alternative analytical approach to the current use of safety factors and deterministic methods for Hg TMDL decision support, one that is fully compatible with an adaptive management approach. This alternative approach uses empirical data and informed judgment to provide a scientific and technical basis for helping National Pollutant Discharge Elimination System (NPDES) permit holders make management decisions. An Hg-offset system would be an option if a wastewater-treatment plant could not achieve NPDES permit requirements for HgT reduction. We develop a probabilistic decision-analytical model consisting of three submodels for HgT loading, MeHg, and cost mitigation within a Bayesian network that integrates information of varying rigor and detail into a simple model of a complex system. Hg processes are identified and quantified by using a combination of historical data, statistical models, and expert judgment. Such an integrated approach to uncertainty analysis allows easy updating of prediction and inference when observations of model variables are made. We demonstrate our approach with data from the Cache Creek watershed (a subbasin of the Sacramento River watershed). The empirical models used to generate the needed probability distributions are based on the same empirical models currently being used by the Central Valley Regional Water Quality Control Cache Creek Hg TMDL working group. The significant difference is that input uncertainty and error are explicitly included in the model and propagated throughout its algorithms. This work demonstrates how to integrate uncertainty into the complex and highly uncertain Hg TMDL decisionmaking process. The various sources of uncertainty are propagated as decision risk that allows decisionmakers to simultaneously consider uncertainties in remediation/implementation costs while attempting to meet environmental/ecologic targets. We must note that this research is on going. As more data are collected, the HgT and cost-mitigation submodels are updated and the uncertainties may be reduced. Subsequently, the value of using a probabilistic framework for estimating and explicitly stating these uncertainties within a decisionmaking process can be estimated when new data are collected. Future work includes the design and implementation of a Bayesian network decision support system (BN-DSS) to produce mitigation scenarios for offset-project evaluation in the Cache Creek watershed. The decisionmaker, a wastewater-treatment plant, is expected to evaluate potential Hg-offset programs in terms of changes in HgT load changes, MeHg-production potential, project cost, and other suitability criteria. Subsequently, scenarios can be analyzed by performing sensitivity analyses and ranking environmental and economic uncertainties in terms of the decisionmaker’s preferences and risk choices. Such an analysis allows decisionmakers and stakeholders to explore various scenarios and predict the consequences of different stated preferences over outcomes.

Open-File Report