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U.S. Geological Survey science vision for native freshwater mussel research in the United States

Executive Summary North America is a global center for native freshwater mussel (order Unionida, hereinafter “mussels”) diversity, with more than 350 species. Mussels are among the most imperiled fauna on the planet. Reasons for both local and widespread declines in mussels are mostly unknown, although the threats may include habitat loss and fragmentation, diseases, environmental contaminants, altered flow regimes, migration barriers to larval hosts, non-native species, and climate change. Over the past three decades, research on mussels has been substantial. Nevertheless, current conservation and management efforts are limited by significant information gaps. For example, the effects of emerging stressors on mussels are largely unknown and identifying when habitats are rehabilitated and suitable for reestablishment of mussels remains challenging. Additionally, historical and current information on the distribution, taxonomy, and life histories are often unreliable or lacking altogether, and more reliable information is needed for many species. We identified focal research themes, goals, and objectives where research on mussels is needed based on information gaps identified through conversations with resource partners across local, regional, and national organizations. Research on biodiversity seeks to enhance the diversity of mussel species and populations to support healthy aquatic ecosystems. Research on emerging stressors seeks to improve the understanding of how mussel species, populations, and communities respond to emerging stressors, including environmental contaminants and climate change. Research on conservation seeks to enhance the recovery of species and populations and to identify data gaps limiting the conservation of mussels and their habitats. Mussels are in urgent need of proactive conservation because they are an integral part of our natural heritage, enhance biodiversity, and provide vital ecological services that support freshwater ecosystems. The U.S. Geological Survey (USGS) has been, and continues to be, a leader in mussel research. Although the USGS is well suited to address the broad-scale multidisciplinary research needed to conserve mussels, the USGS has had substantial loss of scientists with mussel expertise over the past 20 years. However, the breadth of the USGS expertise on mussels can be leveraged internally across other USGS mission and program areas and externally across research partners. Given the breadth and scope of the issues facing mussels across the United States, the research themes outlined in this science vision can only be accomplished through extensive collaborations between the USGS and the full spectrum of natural resource partners, including other Federal and State agencies, Tribal organizations, universities, industries, and nongovernmental organizations.

Circular↗

Recent advances in environmental flows science and water management—Innovation in the Anthropocene

The implementation of environmental flow regimes offers a promising means to protect and restore riverine, wetland and estuarine ecosystems, their critical environmental services and cultural/societal values. This Special Issue expands the scope of environmental flows and water science in theory and practice, offering 20 papers from academics, agency researchers and non‐governmental organisations, each with fresh perspectives on the science and management of environmental water allocations. Contributions confront the grand challenge for environmental flows and water management in the Anthropocene—the urgent need for innovations that will help to sustain the innate resilience of social–ecological systems under dynamic and uncertain environmental and societal futures. Basin‐scale and regional assessments of flow requirements mark a necessary advance in environmental water science in the face of rapid changes in water‐resource management activities worldwide (e.g. increases in dams, diversions, retention and reuse). Techniques for regional‐scale hydrological and ecohydrological modelling support ecological risk assessment and identification of priority flow management and river restoration actions. Changing flood–drought cycles, long‐term climatic shifts and associated effects on hydrological, thermal and water quality regimes add enormous uncertainty to the prediction of future ecological outcomes, regardless of environmental water allocations. An improved capacity to predict the trajectories of ecological change in rivers degraded by legacies of past impact interacting with current conditions and future climate change is essential. Otherwise, we risk unrealistic expectations from restoration of river and estuarine flow regimes. A more robust, dynamic and predictive approach to environmental water science is emerging. It encourages the measurement of process rates (e.g. birth rate, colonisation rate) and species traits (e.g. physiological requirements, morphological adaptations) as well as ecosystem states (e.g. species richness, assemblage structure), as the variables representing ecological responses to flow variability and environmental water allocations. Another necessary development is the incorporation of other environmental variables such as water temperature and sedimentary processes in flow–ecological response models. Based on contributions to this Special Issue, several recent compilations and the wider literature, we identify six major scientific challenges for further exploration, and seven themes for advancing the management of environmental water. We see the emerging frontier of environmental flows and water science as urgent and challenging, with numerous opportunities for reinvigorated science and methodological innovation in the expanding enterprise of environmental water linked to ecological sustainability and social well‐being.

Freshwater Biology↗

Transforming ecosystems: When, where, and how to restore contaminated sites

Chemical contamination has impaired ecosystems, reducing biodiversity and the provisioning of functions and services. This has spurred a movement to restore contaminated ecosystems and develop and implement national and international regulations that require it. Nevertheless, ecological restoration remains a young and rapidly growing discipline and its intersection with toxicology is even more nascent and underdeveloped. Consequently, we provide guidance to scientists and practitioners on when, where, and how to restore contaminated ecosystems. Although restoration has many benefits, it also can be expensive, and in many cases systems can recover without human intervention. Hence, the first question we address is: “When should we restore contaminated ecosystems?” Second, we provide suggestions on what to restore—biodiversity, functions, services, all 3, or something else—and where to restore given expected changes to habitats driven by global climate change. Finally, we provide guidance on how to restore contaminated ecosystems. To do this, we analyze critical aspects of the literature dealing with the ecology of restoring contaminated ecosystems. Additionally, we review approaches for translating the science of restoration to on-the-ground actions, which includes discussions of market incentives and the finances of restoration, stakeholder outreach and governance models for ecosystem restoration, and working with contractors to implement restoration plans. By explicitly considering the mechanisms and strategies that maximize the success of the restoration of contaminated sites, we hope that our synthesis serves to increase and improve collaborations between restoration ecologists and ecotoxicologists and set a roadmap for the restoration of contaminated ecosystems.

Integrated Environmental Assessment and Management↗

Plant community predictions support the potential for big sagebrush range expansion adjacent to the leading edge

Big sagebrush ecosystems are widespread across drylands of western North America and provide numerous services, but the abundance of these ecosystems has declined substantially and the future of these ecosystems is uncertain. As a result, characterizing potential areas for expansion of these ecosystems is important. Species distribution models of the big sagebrush suggest areas of increasing climatic habitat suitability at northern latitudes under climate change scenarios. This implies the formation of a leading edge during a future big sagebrush range expansion. Such an expansion requires that current nearby range margin big sagebrush populations are stable and serve as future seed sources. Our goal was to quantify the impacts of future climate conditions on the plant community composition and biomass in the in range margin big sagebrush plant communities adjacent to the leading edge. We did this using an individual-based soil water and plant growth simulation model, STEPWAT2. We assessed community dynamics throughout the twenty-first century using 13 climate models under two representative concentration pathways to capture the variability among projections. Our results show minimal overall change in plant community composition and little change in biomass, suggesting that range margin big sagebrush plant communities adjacent to the leading edge will remain stable to serve as essential dispersal sources for future range expansion, assuming no other relevant changes such as changes in disturbance regimes. These assessments of plant community responses to shifts in climate and characterization of variability in future projections will help inform conservation planning and management of the big sagebrush ecosystem.

Regional Environmental Change↗

The Chesapeake Bay program modeling system: Overview and recommendations for future development

The Chesapeake Bay is the largest, most productive, and most biologically diverse estuary in the continental United States providing crucial habitat and natural resources for culturally and economically important species. Pressures from human population growth and associated development and agricultural intensification have led to excessive nutrient and sediment inputs entering the Bay, negatively affecting the health of the Bay ecosystem and the economic services it provides. The Chesapeake Bay Program (CBP) is a unique program formally created in 1983 as a multi-stakeholder partnership to guide and foster restoration of the Chesapeake Bay and its watershed. Since its inception, the CBP Partnership has been developing, updating, and applying a complex linked modeling system of watershed, airshed, and estuary models as a planning tool to inform strategic management decisions and Bay restoration efforts. This paper provides a description of the 2017 CBP Modeling System and the higher trophic level models developed by the NOAA Chesapeake Bay Office, along with specific recommendations that emerged from a 2018 workshop designed to inform future model development. Recommendations highlight the need for simulation of watershed inputs, conditions, processes, and practices at higher resolution to provide improved information to guide local nutrient and sediment management plans. More explicit and extensive modeling of connectivity between watershed landforms and estuary sub-areas, estuarine hydrodynamics, watershed and estuarine water quality, the estuarine-watershed socioecological system, and living resources will be important to broaden and improve characterization of responses to targeted nutrient and sediment load reductions. Finally, the value and importance of maintaining effective collaborations among jurisdictional managers, scientists, modelers, support staff, and stakeholder communities is emphasized. An open collaborative and transparent process has been a key element of successes to date and is vitally important as the CBP Partnership moves forward with modeling system improvements that help stakeholders evolve new knowledge, improve management strategies, and better communicate outcomes.

Chesapeake Bay estuary and watershed↗

A multidisciplinary coastal vulnerability assessment for local government focused on ecosystems, Santa Barbara area, California

Incorporating coastal ecosystems in climate adaptation planning is needed to maintain the well-being of both natural and human systems. Our vulnerability study uses a multidisciplinary approach to evaluate climate change vulnerability of an urbanized coastal community that could serve as a model approach for communities worldwide, particularly in similar Mediterranean climates. We synthesize projected changes in climate, coastal erosion and flooding, watershed runoff and impacts to two important coastal ecosystems, sandy beaches and coastal salt marshes. Using downscaled climate models along with other regional models, we find that temperature, extreme heat events, and sea level are expected to increase in the future, along with more intense rainfall events, despite a negligible change in annual rainfall. Consequently, more droughts are expected but the magnitude of larger flood events will increase. Associated with the continuing rise of mean sea level, extreme coastal water levels will occur with increasingly greater magnitudes and frequency. Severe flooding will occur for both natural (wetlands, beaches) and built environments (airport, harbor, freeway, and residential areas). Adaptation actions can reduce the impact of rising sea level, which will cause losses of sandy beach zones and salt marsh habitats that support the highest biodiversity in these ecosystems, including regionally rare and endangered species, with substantial impacts occurring by 2050. Providing for inland transgression of coastal habitats, effective sediment management, reduced beach grooming and removal of shoreline armoring are adaptations that would help maintain coastal ecosystems and the beneficial services they provide.

California↗

LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes

Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states. LAGOS-NE contains data for 51 101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past 3 decades for approximately 2600–12 000 lakes depending on the variable. The database contains approximately 150 000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from 87 lake water quality data sets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest and most comprehensive databases of its type because it includes both in situ measurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales.

Connecticut, Iowa, Illinois, Indiana, Massachusett↗

Coastal wetlands: an integrated ecosystem approach

Coastal wetlands are under a great deal of pressure from the dual forces of rising sea level and the intervention of human populations both along the estuary and in the river catchment. Direct impacts include the destruction or degradation of wetlands from land reclamation and infrastructures. Indirect impacts derive from the discharge of pollutants, changes in river flows and sediment supplies, land clearing, and dam operations. As sea level rises, coastal wetlands in most areas of the world migrate landward to occupy former uplands. The competition of these lands from human development is intensifying, making the landward migration impossible in many cases. This book provides an understanding of the functioning of coastal ecosystems and the ecological services that they provide, and suggestions for their management. In this book a CD is included containing color figures of wetlands and estuaries in different parts of the world.

Book↗

Demographic studies of Joshua trees in Mojave Desert National Parks: demography with emphasis on germination and recruitment

The study of population change with regard to reproduction, seed dispersal, and germination, establishment, growth, and survival/mortality is known as demography. Demographic studies provide managers with information to assess future trends on the density, distribution, health, and population changes of importance or value, including Joshua trees (Yucca brevifolia). Demographic research provides the potential to understand the combined impacts of climate change and land-use practices and determine if strategies for protecting important species are likely to succeed or fall short of management goals and will identify factors that have the potential to de-stabilize populations outside the realm of natural variation so that management strategies can be developed to circumvent challenges for key species, processes, and ecosystems. The National Park Service and US Geological Survey are collaborating to collect demographic information about the demographics of Joshua tree in the Mojave Desert.

Arizona;California;Nevada↗

Coastal systems and low-lying areas

Since the IPCC Third Assessment Report (TAR), our understanding of the implications of climate change for coastal systems and low-lying areas (henceforth referred to as ‘coasts’) has increased substantially and six important policy-relevant messages have emerged. Coasts are experiencing the adverse consequences of hazards related to climate and sea level (very high confidence). Coasts are highly vulnerable to extreme events, such as storms, which impose substantial costs on coastal societies [6.2.1, 6.2.2, 6.5.2]. Annually, about 120 million people are exposed to tropical cyclone hazards, which killed 250,000 people from 1980 to 2000 [6.5.2]. Through the 20th century, global rise of sea level contributed to increased coastal inundation, erosion and ecosystem losses, but with considerable local and regional variation due to other factors [6.2.5, 6.4.1]. Late 20th century effects of rising temperature include loss of sea ice, thawing of permafrost and associated coastal retreat, and more frequent coral bleaching and mortality [6.2.5]. Coasts will be exposed to increasing risks, including coastal erosion, over coming decades due to climate change and sea-level rise (very high confidence). Anticipated climate-related changes include: an accelerated rise in sea level of up to 0.6 m or more by 2100; a further rise in sea surface temperatures by up to 3°C; an intensification of tropical and extra-tropical cyclones; larger extreme waves and storm surges; altered precipitation/run-off; and ocean acidification [6.3.2]. These phenomena will vary considerably at regional and local scales, but the impacts are virtually certain to be overwhelmingly negative [6.4, 6.5.3]. Corals are vulnerable to thermal stress and have low adaptive capacity. Increases in sea surface temperature of about 1 to 3°C are projected to result in more frequent coral bleaching events and widespread mortality, unless there is thermal adaptation or acclimatisation by corals [Box 6.1, 6.4]. Coastal wetland ecosystems, such as saltmarshes and mangroves, are especially threatened where they are sediment starved or constrained on their landward margin [6.4.1]. Degradation of coastal ecosystems, especially wetlands and coral reefs, has serious implications for the well-being of societies dependent on the coastal ecosystems for goods and services [6.4.2, 6.5.3]. ncreased flooding and the degradation of freshwater, fisheries and other resources could impact hundreds of millions of people, and socio-economic costs on coasts will escalate as a result of climate change [6.4.2, 6.5.3]. The impact of climate change on coasts is exacerbated by increasing human-induced pressures (very high confidence). Utilisation of the coast increased dramatically during the 20th century and this trend is virtually certain to continue through the 21st century. Under the SRES scenarios, the coastal population could grow from 1.2 billion people (in 1990) to 1.8 to 5.2 billion people by the 2080s, depending on assumptions about migration [6.3.1]. Increasing numbers of people and assets at risk at the coast are subject to additional stresses due to land-use and hydrological changes in catchments, including dams that reduce sediment supply to the coast [6.3.2]. Populated deltas (especially Asian megadeltas), low-lying coastal urban areas and atolls are key societal hotspots of coastal vulnerability, occurring where the stresses on natural systems coincide with low human adaptive capacity and high exposure [6.4.3]. Regionally, South, South- East and East Asia, Africa and small islands are most vulnerable [6.4.2]. Climate change therefore reinforces the desirability of managing coasts in an integrated manner [6.6.1.3]. Adaptation for the coasts of developing countries will be more challenging than for coasts of developed countries, due to constraints on adaptive capacity (high confidence). While physical exposure can significantly influence vulnerability for both human populations and natural systems, a lack of adaptive capacity is often the most important factor that creates a hotspot of human vulnerability. Adaptive capacity is largely dependent upon development status. Developing nations may have the political or societal will to protect or relocate people who live in low-lying coastal zones, but without the necessary financial and other resources/capacities, their vulnerability is much greater than that of a developed nation in an identical coastal setting. Vulnerability will also vary between developing countries, while developed countries are not insulated from the adverse consequences of extreme events [6.4.3, 6.5.2]. Adaptation costs for vulnerable coasts are much less than the costs of inaction (high confidence). Adaptation costs for climate change are much lower than damage costs without adaptation for most developed coasts, even considering only property losses and human deaths [6.6.2, 6.6.3]. As post-event impacts on coastal businesses, people, housing, public and private social institutions, natural resources, and the environment generally go unrecognised in disaster cost accounting, the full benefits of adaptation are even larger [6.5.2, 6.6.2]. Without adaptation, the high-end sea-level rise scenarios, combined with other climate changes (e.g., increased storm intensity), are as likely as not to render some islands and lowlying areas unviable by 2100, so effective adaptation is urgently required [6.6.3]. The unavoidability of sea-level rise, even in the longer-term, frequently conflicts with present-day human development patterns and trends (high confidence). Sea-level rise has substantial inertia and will continue beyond 2100 for many centuries. Irreversible breakdown of the West Antarctica and/or Greenland ice sheets, if triggered by rising temperatures, would make this long-term rise significantly larger, ultimately questioning the viability of many coastal settlements across the globe. The issue is reinforced by the increasing human use of the coastal zone. Settlement patterns also have substantial inertia, and this issue presents a challenge for long-term coastal spatial planning. Stabilisation of climate could reduce the risks of ice sheet breakdown, and reduce but Chapter 6 Coastal systems and low-lying areas 317 not stop sea-level rise due to thermal expansion [Box 6.6]. Hence, it is now more apparent than it was in the TAR that the most appropriate response to sea-level rise for coastal areas is a combination of adaptation to deal with the inevitable rise, and mitigation to limit the long-term rise to a manageable level [6.6.5, 6.7].

Book chapter↗

Ecological consequences of changing hydrological conditions in wetland forests of coastal Louisiana

Large-scale and localized alterations of processes affecting deltaic coastal wetlands have caused the complete loss of some coastal wetland forests and reduced the productivity and vigor of many areas in coastal Louisiana. This loss and degradation threatens ecosystem functions and the services they provide. This paper summarizes ecological relationships controlled by hydrological processes in coastal wetland forests of the Mississippi River delta and presents two case studies that illustrate the complexity of assessing hydrological control on swamp forest establishment and growth. Productivity of overstory trees has been affected by these changes, but the first case study illustrates that the relationship between flooding and growth may be site-specific. An important effect of increased flooding has been to reduce regeneration of swamp forest trees. The second case study is an outline of the kind of hydrological analysis required to assess probability of regeneration success.

Louisiana↗

Benthic infaunal communities of Baltimore and Norfolk Canyons

The imperative for finding, cataloging, and understanding continental margin diversity derives from the many key functions, goods and services provided by margin ecosystems and by an increasingly deleterious human footprint on our continental slopes (Levin and Dayton 2009). Progress in seafloor mapping technology and direct observation has revealed unexpected heterogeneity, with a mosaic of habitats and ecosystems linked to geomorphological, geochemical, and hydrographic features that are capable of influencing biotic diversity (Levin and Sibuet 2012). Submarine canyons are dramatic and widespread topographic features crossing continental and island margins in oceans, connecting shelf-margins to deep ocean basins (Harris and Whiteway 2011). Their importance as biodiversity hotspots has continued to emerge over the last two decades as research efforts have increased. Understanding the physical parameters within a canyon system is a primary factor for understanding habitat variability and ecological patterns within the confines of canyon systems (Levin et al. 2001). Margin sediments exhibit ubiquitous depth zonation (Carney et al. 2005), with a diverse suite of species that occupy restricted bathymetric ranges along any given section of the margin. Major shifts in composition among taxa are observed at the shelf-slope transition zone (canyons <500 m), along the upper slope (1,000 m), and at the lower slope transition zone (<3,000 m) (Gibson et al. 2005). In the deep sea, macrofaunal assemblages are generally limited by the availability of allochthonous organic material (Rowe et al. 1982, Billet et al. 1983, Rex et al. 2005, Smith et al. 2008) where macrofaunal densities usually decline with depth and distance from the shore (Rowe et al. 1982, Houston and Haedrich 1984, Rex et al. 2005). However, canyon fauna can experience enhanced food supply through the resuspension and deposition of organic-rich sediments, delivered by increased current velocities within the confines of the canyon (Rowe 1971, Shepard et al. 1974). As a result, canyons are often reported as sustaining enhanced abundances and biomass compared with nearby open slope habitats at similar depths (Vetter and Dayton 1998, Duineveld et al. 2001, De Leo et al. 2010) as well as enhancing regional (γ) and local (α) biodiversity (Hecker et al. 1983, Vetter and Dayton 1998, De Leo et al. 2010, Vetter et al. 2010). Furthermore, enhanced habitat heterogeneity can also be a major structuring agent of ecological assemblages, promoting beta (β) diversity (McClain and Barry 2010) in canyon environments. Canyon systems have often been described as biodiversity hotspots, especially at mid-slope depths (Levin and Sibuet 2012) where physical processes, characterized by complex patterns in hydrography, promote topographically induced upwelling, enhanced mixing via internal tides, and the focusing of tidal bores (Vetter and Dayton 1998, Cacchione et al. 2002). Additionally, sediment transport and accumulation (García et al. 2008) represent important influential ecological drivers. Factors such as substrata heterogeneity (Levin and Sibuet 2012) and concentration of organic matter (De Leo et al. 2010) have been suggested to explain higher faunal diversity, abundance, and benthic productivity found in canyon systems compared with surrounding areas. Bathymetric patterns of species diversity have been attributed to changes in sediment characteristics (Etter and Grassle 1992), productivity, currents, oxygen, disturbance, and the interplay of biotic effects with depth and latitude (Levin et al. 2001, Carney et al. 2005). Recent studies report on the uniqueness of canyon benthic communities and habitats and the view that no two canyons are alike (Cunha et al. 2011). Certain submarine canyons may maintain 436 characteristic and unique faunas, but more often canyon macrofaunal assemblages show high dominance and locally reduced biodiversity (Rowe 1971, Gage 1997, Curdia et al. 2004, Cun

Baltimore Canyon, Norfolk Canyon↗

Global change impacts on mangrove ecosystems

Mangroves are tropical/subtropical communities of primarily tree species that grow in the intertidal zone. These tidal forests are important coastal ecosystems that are valued for a variety of ecological and societal goods and services. Major local threats to mangrove ecosystems worldwide include clearcutting and trimming of forests for urban, agricultural, or industrial expansion; hydrological alterations; toxic chemical spills; and eutrophication. In many countries with mangroves, much of the human population resides in the coastal zone, and their activities often negatively impact the integrity of mangrove forests. In addition, eutrophication, which is the process whereby nutrients build up to higher than normal levels in a natural system, is possibly one of the most serious threats to mangroves and associated ecosystems such as coral reefs. Scientists with the U.S. Geological Survey (USGS) at the National Wetlands Research Center are working to more fully understand global impacts on these significant ecosystems. Changes in climate and other factors may also affect mangroves, but in complex ways. Global warming may promote expansion of mangrove forests to higher latitudes and accelerate sea-level rise through melting of polar ice or steric expansion of oceans. Changes in sea level would alter flooding patterns and the structure and areal extent of mangroves. Climate change may also alter rainfall patterns, which would in turn change local salinity regimes and competitive interactions of mangroves with other wetland species. Increases in frequency or intensity of tropical storms and hurricanes in combination with sea-level rise may alter erosion and sedimentation rates in mangrove forests. Another global change factor that may directly affect mangrove growth is increased atmospheric carbon dioxide (CO 2 ), caused by burning of fossil fuels and other factors. Elevated CO 2 concentration may increase mangrove growth by stimulating photosynthesis or improving water use efficiency, but the consequences of this growth enhancement for the ecosystem are unknown.

Fact Sheet↗

Applying concepts of general resilience to large river ecosystems: A case study from the Upper Mississippi and Illinois rivers

Large floodplain-river ecosystems are often highly modified to provide services that society desires, yet these modifications can limit an ecosystem’s ability to adapt to changing conditions. The adaptive capacity of an ecosystem, its general resilience, is a conceptual framework for considering how a system will respond to such changes. We sought to apply aspects of three general resilience principles (diversity and redundancy, connectivity, and controlling variables) to our understanding of floodplain-river ecosystem structure and function. We demonstrate the applicability of this approach in a case study of the Upper Mississippi River System (UMRS). In doing so, we developed ten indicators that highlight important structural and functional aspects of this floodplain-river ecosystem, and likely underlie the capacity of large rivers to cope with environmental change and disturbance. We developed diversity and redundancy indicators for aquatic habitats, patterns of floodplain inundation, and fish communities. Connectivity indicators included metrics of longitudinal and lateral connections. Controlling variable indicators included deviations from historic water surface elevation fluctuations, water clarity, nutrient concentrations, and aquatic invasive species. This set of indicators provides a simple description of the adaptive capacity of four distinct reaches of the UMRS: Upper Impounded, Lower Impounded, Unimpounded Reaches of the Upper Mississippi River and the entire Illinois River. High aquatic habitat diversity and redundancy, fish functional diversity and redundancy, and water clarity, and the scarcity of invasive fish species are all factors that likely contribute to the high general resilience of the Upper Impounded Reach. However, the limited longitudinal connectivity and establishment of a minimum water level for navigation are factors that may inhibit the general resilience of this reach. In the Lower Impounded Reach, there is high within-reach variability for individual indicators such as aquatic habitat diversity, fish functional diversity and redundancy, and longitudinal and lateral connectivity. In the Unimpounded Reach, a high degree of longitudinal connectivity likely enhances its general resilience, but low aquatic habitat diversity, low lateral connectivity, and relatively high number of invasive fish species inhibit general resilience. For the Illinois River Reach, the relatively high fish functional diversity and redundancy likely contributes to its general resilience, whereas high number of invasive fish species, low water clarity, low lateral connectivity, and high range of water levels may inhibit general resilience. Indicators derived from application of concepts of general resilience provide insight into the current coping capacity of the UMRS and identify opportunities for enhancing resilience.

Upper Mississippi River System↗

Biocomplexity in mangrove ecosystems

Mangroves are an ecological assemblage of trees and shrubs adapted to grow in intertidal environments along tropical coasts. Despite repeated demonstration of their economic and societal value, more than 50% of the world's mangroves have been destroyed, 35% in the past two decades to aquaculture and coastal development, altered hydrology, sea-level rise, and nutrient overenrichment. Variations in the structure and function of mangrove ecosystems have generally been described solely on the basis of a hierarchical classification of the physical characteristics of the intertidal environment, including climate, geomorphology, topography, and hydrology. Here, we use the concept of emergent properties at multiple levels within a hierarchical framework to review how the interplay between specialized adaptations and extreme trait plasticity that characterizes mangroves and intertidal environments gives rise to the biocomplexity that distinguishes mangrove ecosystems. The traits that allow mangroves to tolerate variable salinity, flooding, and nutrient availability influence ecosystem processes and ultimately the services they provide. We conclude that an integrated research strategy using emergent properties in empirical and theoretical studies provides a holistic approach for understanding and managing mangrove ecosystems.

Annual Review of Marine Science↗

Effects of Hydrocarbon Extraction on Landscapes of the Appalachian Basin

An important and sometimes overlooked aspect of contemporary natural gas exploration, development, and delivery activities is the geographic profile and spatial footprint that these activities have on the land surface. The function of many ecosystems and the goods and services they provide, in large part, are the result of their natural spatial arrangement on the landscape. Shale-gas development can create alterations to the pattern of land use and land cover, and represents a specific form of land use and land cover change that can substantially impact critical aspects of the spatial pattern, form, and function of landscape interactions, including many biological responses. The need for energy resources has created numerous economic opportunities for hydrocarbon extraction in the Appalachian basin. The development of alternative energy natural gas resources from deep-shale drilling techniques, along with conventional natural gas extraction methods, has created a flurry of wells, roads, pipelines, and related infrastructure across many parts of the region. An unintended and sometimes overlooked consequence of these activities is their effect on the structure and function of the landscape and ecosystems. The collective effect of over 100,000 hydrocarbon extraction permits for oil, coal bed methane, Marcellus and Utica Shale natural gas wells, and other types of hydrocarbon gases and their associated infrastructure has saturated much of the landscape and disturbed the natural environment in the Appalachian basin. The disturbance created by the sheer magnitude of the development of these collective wells and infrastructure directly affects how the landscape and ecosystems function and how they provide ecological goods and services.

New York, Ohio, Pennsylvania, Virginia, West Virgi↗

Solar and sensor geometry, not vegetation response, drive satellite NDVI phenology in widespread ecosystems of the western United States

Satellite-derived phenology metrics are valuable tools for understanding broad-scale patterns and changes in vegetated landscapes over time. However, the extraction and interpretation of phenology in ecosystems with subtle growth dynamics can be challenging. US National Park Service monitoring of evergreen pinyon-juniper ecosystems in the western US revealed an unexpected winter-peaking phenological pattern in normalized difference vegetation index (NDVI) time-series derived from Moderate Resolution Imaging Spectroradiometer (MODIS) imagery. In this paper, we assess the validity of the winter peaks through ground-based observation of phenology and examination of solar and satellite geometry effects. To test the premise of a true vegetation response, we analyzed NDVI values extracted from a time series of ground-based digital camera (‘phenocam’) images collected September 2017 to December 2018 in a pinyon-juniper woodland in Arizona, US. Results show pinyon and juniper growth peaked in the warm season, as did the other species in the phenocam field of view. NDVI time series from four other sensors (Landsat 7, Sentinel-2, VIIRS, and Proba-V) confirmed that winter peaks in this ecosystem are not limited to MODIS products. Examination of NDVI time series (2003–2018) derived from daily 250-m MODIS data in the broader pinyon-juniper ecosystem revealed that solar-to-sensor angle, sensor zenith angle, and forward/back-scatter reflectance explained >80% of intra-annual variability. Solar-to-sensor angle exerted the greatest control, and the direction of its correlation (positive) was the opposite of that which would be expected if it were driven by vegetation greenness. Solar-to-sensor angle is controlled seasonally by solar zenith angle and daily by variations in satellite overpass geometry. We mapped winter peaks across the western US in Google Earth Engine using 500-m MODIS MCD43A4 data, which correct for reflectance differences caused by view angle. In areas where winter vegetation peaks are ecologically improbable (i.e., locations with sub-freezing December temperatures), consistent winter peaks (≥ 14 years in 2003 to 2018) are widespread in both pinyon-juniper and non-pinyon-juniper conifer ecosystems; winter peaks are common (≥ 5 years in 2003 to 2018) across areas of shrubland. We attribute winter peaks to the positive correlation of NDVI with solar-to-sensor angle and solar zenith angle in combination with sparse, vertically oriented evergreen vegetation canopies. Increasing shadow visibility has been shown to increase overall NDVI, and the prevalence of the winter peaking in evergreen western sparse canopy ecosystems is consistent with this hypothesis. The extent of winter peaking patterns may have been previously overlooked due to temporal compositing, curve fitting, and incomplete snow screening.

Arizona, California, Colorado, Idaho, Montana, Nev↗

Cooperative Fish and Wildlife Research Units program—2018 year in review

The Cooperative Fish and Wildlife Research Units (CRU) program had an interesting and challenging year in 2018. We made significant strategic advances on many fronts and had setbacks in others. Our relationship with the U.S. Fish and Wildlife Service, the agency we belonged to from 1935 to the mid-1990s, was further reinforced through strategic efforts with the Service’s Science Applications senior staff. This is bearing fruit in terms of research collaborations and funding support. As part of a larger effort between the U.S. Geological Survey (USGS) Ecosystems Mission Area and the Service’s endangered species program, we are also collaborating to address science needs for species in pre-listing status. Barry Grand, Unit Supervisor (South), has been instrumental in this effort. Tom Edwards of the Utah Unit has met with representatives of the U.S. Fish and Wildlife Service and the Association of Fish and Wildlife Agencies to promote training of leaders and “hands dirty” biologists in species distribution modeling. The Association passed a unanimous resolution endorsing the training at their midyear meeting in March. Tom held a workshop at the annual meeting of the Association of Fish and Wildlife Agencies in September, and future workshops, supported by the U.S. Fish and Wildlife Service, will be held bringing State agency and U.S. Fish and Wildlife Service biologists together to work on species of common concern. Wyoming Unit Leader Matt Kauffman’s pioneering work in identifying and mapping big-game migration corridors has captured the attention of conservationists far and wide. In the spring, the Secretary of the Interior signed Secretarial Order No. 3362, "Improving Habitat Quality in Western Big-Game Winter Range and Migration Corridors" directing efforts of several U.S. Department of the Interior (DOI) bureaus to collaborate with States in identifying and protecting big-game corridors in 11 States. Matt has conducted several workshops that directly support the Secretarial order, and more are planned. Corridor mapping efforts supported by the USGS and the DOI, based in the States and coordinated by Matt, are unfolding. Unit Administrative Officer Shana Coulby and her staff hosted a training program for university support staff at USGS National Headquarters in March. Shana’s team did a superb job, and the camaraderie among all was evident. We co-sponsored the third in a series of workshops at the North American Wildlife and Natural Resources Conference in March on bridging the gap between science and management. The State Department requested that we coordinate a workshop that would bring CRU scientists and other U.S. representatives together with Brazilian, Colombian, and Peruvian scientists and decision makers to develop best practices to minimize environmental damage from infrastructure development in the Amazon and to collaborate on science needs. The workshop was held in Iquitos, Peru, in the heart of the Amazon during August. Our cooperator community, represented by the National Cooperators Coalition, was very active in response to the President’s budget proposal that would have redirected funding for the CRU program to other priorities. Their efforts are reflected in the House and Senate marks on the fiscal year 2019 budget that not only restored funding, but recommended increases. You will see in this report many other accomplishments of our individual scientists and students during 2018. It was an impressive and productive year! What you won’t see chronicled is the work of the CRU headquarters staff and University support staff. These folks are extraordinary in their dedication to working with cooperators and scientists to solve problems and ensure the important work gets accomplished with minimal interference. We are truly fortunate to have such skilled and dedicated folks in the trenches. I was fortunate to visit several units during 2018. For me, this is the most enriching part of my duties. I get to see firsthand the work our scientists do, the incredible students being mentored, and meet our cooperators on their turf. As we look forward towards the horizon, 2019 looks brighter for the CRU program. Efforts by our cooperators to generate support for filling our vacancies are materializing. Our cadre of scientists is second to none, and the breadth and depth of our work are nothing short of impressive. Thanks to all who are part of this cooperative endeavor—conservation is the ultimate winner in our efforts!

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