Governing Ecological Connectivity in Cross-Scale Dependent Systems.

Ecosystem management and governance of cross-scale dependent systems require integrating knowledge about ecological connectivity in its multiple forms and scales. Although scientists, managers, and policymakers are increasingly recognizing the importance of connectivity, governmental organizations may not be currently equipped to manage ecosystems with strong cross-boundary dependencies. Managing the different aspects of connectivity requires building social connectivity to increase the flow of information, as well as the capacity to coordinate planning, funding, and actions among both formal and informal governance bodies. We use estuaries in particular the San Francisco Estuary, in California, in the United States, as examples of cross-scale dependent systems affected by many intertwined aspects of connectivity. We describe the different types of estuarine connectivity observed in both natural and human-affected states and discuss the human dimensions of restoring beneficial physical and ecological processes. Finally, we provide recommendations for policy, practice, and research on how to restore functional connectivity to estuaries.

Mapping legal authority for terrestrial conservation corridors along streams.

Wildlife corridors aim to promote species' persistence by connecting habitat patches across fragmented landscapes. Their implementation is limited by patterns of land ownership and complicated by differences in the jurisdictional and regulatory authorities under which lands are managed. Terrestrial corridor conservation requires coordination across jurisdictions and sectors subject to site-specific overlapping sources of legal authority. Mapping spatial patterns of legal authority concurrent with habitat condition can illustrate opportunities to build or leverage capacity for connectivity conservation. Streamside areas provide pragmatic opportunities to leverage existing policy mechanisms for riverine and terrestrial habitat connectivity across boundaries. Conservation planners and practitioners can make use of these opportunities by harmonizing actions for multiple conservation outcomes. We formulated an integrative, data-driven method for mapping multiple sources of legal authority weighted by capacity for coordinating terrestrial habitat conservation along streams. We generated a map of capacity to coordinate streamside corridor protections across a wildlife habitat gap to demonstrate this approach. We combined values representing coordination capacity and naturalness to generate an integrated legal-ecological resistance map for connectivity modeling. We then computed least-cost corridors across the integrated map, masking the terrestrial landscape to focus on streamside areas. Streamside least-cost corridors in the integrated, local-scale model diverged (∼25 km) from national-scale least-cost corridors based on naturalness. Spatial categories comparing legal- and naturalness-based resistance values by stream reach highlighted potential locations for building or leveraging existing capacity through spatial coordination of policy mechanisms or restoration actions. Agencies or nongovernmental organizations intending to restore or maintain habitat connectivity across fragmented landscapes can use this approach to inform spatial prioritization and build coordination capacity. Article impact statement: Combined mapping of legal authority and habitat condition reveals capacity to coordinate actions along streams for clean water and wildlife.

Mapeo de la Autoridad Legal para los Corredores Terrestres de Conservación a lo Largo de Ríos Stahl et al. Resumen Los corredores de fauna buscan promover la persistencia de las especies al conectar los fragmentos de hábitat a lo largo de paisajes fragmentados. Su implementación está limitada por los patrones de propiedad de tierras y se complica con las diferencias entre las autoridades jurisdiccionales y regulatorias que las administran. La conservación por corredores terrestres requiere de coordinación entre las jurisdicciones y los sectores sujetos a fuentes de autoridad legal que se traslapan y que son específicas del sitio. El mapeo de los patrones espaciales de la autoridad legal simultánea a la condición del hábitat puede ilustrar oportunidades para construir o hacer uso de la capacidad para la conservación por conectividad. Las áreas adyacentes a los cauces fluviales proporcionan oportunidades prácticas para hacer uso de los mecanismos políticos existentes para la conectividad de hábitats ribereño y terrestre a través de las fronteras. Los planificadores y practicantes de la conservación pueden usar estas oportunidades al armonizar las acciones para múltiples resultados de conservación. Formulamos un método integrativo orientado por los datos para mapear las múltiples fuentes de autoridad legal ponderadas por la capacidad para coordinar la conservación de hábitats terrestres a lo largo de ríos. Generamos un mapa de la capacidad para coordinar los corredores de protección a lo largo de los vacíos en los hábitats de fauna para demostrar esta estrategia. Combinamos los valores por medio de la representación de la capacidad de coordinación y la naturalidad para generar un mapa de resistencia legal y ecológica para el modelado de la conectividad. Después, computamos los corredores de menor costo en todo el mapa integrado, enmascarando el paisaje terrestre para enfocarnos en las áreas adyacentes al cauce fluvial. Los corredores de menor costo adyacentes a los cauces dentro del modelo integrado de escala local difirieron (∼25 km) de los corredores de menor costo basados en la naturalidad a escala nacional. Las categorías espaciales que compararon los valores de resistencia basada en la legalidad y en la naturalidad por alcance del río resaltaron las localidades potenciales para la construcción o el uso de la capacidad existente por medio de la coordinación espacial de los mecanismos de política o de las acciones de restauración. Las agencias y organizaciones no gubernamentales con la intención de restaurar o mantener la conectividad del hábitat en un paisaje fragmentado pueden utilizar esta estrategia para informar la priorización espacial y construir la capacidad de coordinación.

Stream Transport and Retention of Environmental DNA Pulse Releases in Relation to Hydrogeomorphic Scaling Factors.

The DNA of aquatic organisms can be identified in water sampled from freshwater ecosystems to detect species presence. Because these DNA-based methods (termed environmental DNA, eDNA) confirm species presence by proxy of DNA in water, the processes influencing eDNA transport and removal from water are critical to the method's efficacy and interpretation of results. Previous studies of aquatic eDNA transport and fate have employed uncontrolled field experiments, controlled studies in experimental streams, and laboratory column tests. As a step toward understanding the processes controlling eDNA transport and retention, we released and tracked experimental pulses of white sturgeon eDNA (novel to the system) in five fourth-order stream reaches with varied hydrology and geomorphology. We found strong support that stream water transient storage controls eDNA areal uptake rate (or spiraling length). We calculated the median spiraling length to be ∼260 m. Down channel slope correlated with transient storage, suggesting that this slope could be used as a proximate measure of eDNA removal into the benthic zone. Our results suggest that sampling effort should be increased in reaches with longer transient storage (or lower slopes) to compensate for the increase in eDNA retention.

Degradation and dispersion limit environmental DNA detection of rare amphibians in wetlands: Increasing efficacy of sampling designs.

The detection of rare macroorganisms using environmental DNA (eDNA) is a powerful new method for conservation and management; the efficacy of this method is affected by physiological, ecological, and hydrological processes. Understanding the processes limiting eDNA detection and accounting for those factors with optimized sampling designs is critical for realizing the potential of this tool. Amphibians are a focus of conservation programs globally and are often difficult to detect, presenting a challenge for effective action. To increase the ability of eDNA techniques to inform conservation and management programs, we investigated the eDNA detection of amphibians compared with field surveys for six species across a gradient of environmental factors expected to affect eDNA detection in three different systems: perennial wetlands, intermittent wetlands, and acidic intermittent wetlands. We applied a baseline sampling design in each wetland and used an occupancy modeling approach to evaluate evidence for processes limiting detection for each species given the presence of the target species. Evidence weights indicated that limiting processes varied across systems and included those associated with increased degradation (pH<5, temperature>25°C) and limited dispersion (wetland area>1200m2, sample volume<200mL). Optimized sampling protocols based on model results included an increased number of sampling locations in large and highly degradative (acidic) wetlands and increased filter pore size in high-particulate systems. These improved designs compensated for the previously limiting factors and yielded average detection rates of 0.62-0.86 per water sample. Degradation and dispersion processes appear to strongly influence the detection of amphibians in wetlands. Optimized, adaptive sampling designs can greatly increase the efficacy of eDNA monitoring approaches.

Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa.

Temperate ectomycorrhizal (ECM) fungi show segregation whereby some species dominate in organic layers and others favor mineral soils. Weak layering in tropical soils is hypothesized to decrease niche space and therefore reduce the diversity of ectomycorrhizal fungi. The Neotropical ECM tree Dicymbe corymbosa forms monodominant stands and has a distinct physiognomy with vertical crown development, adventitious roots and massive root mounds, leading to multi-stemmed trees with spatially segregated rooting environments: aerial litter caches, aerial decayed wood, organic root mounds and mineral soil. We hypothesized that these microhabitats host distinct fungal assemblages and therefore promote diversity. To test our hypothesis, we sampled D. corymbosa ectomycorrhizal root tips from the four microhabitats and analyzed community composition based on pyrosequencing of fungal internal transcribed spacer (ITS) barcode markers. Several dominant fungi were ubiquitous but analyses nonetheless suggested that communities in mineral soil samples were statistically distinct from communities in organic microhabitats. These data indicate that distinctive rooting zones of D. corymbosa contribute to spatial segregation of the fungal community and likely enhance fungal diversity.

Regime shifts and panarchies in regional scale social-ecological water systems.

In this article we summarize histories of nonlinear, complex interactions among societal, legal, and ecosystem dynamics in six North American water basins, as they respond to changing climate. These case studies were chosen to explore the conditions for emergence of adaptive governance in heavily regulated and developed social-ecological systems nested within a hierarchical governmental system. We summarize resilience assessments conducted in each system to provide a synthesis and reference by the other articles in this special feature. We also present a general framework used to evaluate the interactions between society and ecosystem regimes and the governance regimes chosen to mediate those interactions. The case studies show different ways that adaptive governance may be triggered, facilitated, or constrained by ecological and/or legal processes. The resilience assessments indicate that complex interactions among the governance and ecosystem components of these systems can produce different trajectories, which include patterns of (a) development and stabilization, (b) cycles of crisis and recovery, which includes lurches in adaptation and learning, and (3) periods of innovation, novelty, and transformation. Exploration of cross scale (Panarchy) interactions among levels and sectors of government and society illustrate that they may constrain development trajectories, but may also provide stability during crisis or innovation at smaller scales; create crises, but may also facilitate recovery; and constrain system transformation, but may also provide windows of opportunity in which transformation, and the resources to accomplish it, may occur. The framework is the starting point for our exploration of how law might play a role in enhancing the capacity of social-ecological systems to adapt to climate change.

Balancing stability and flexibility in adaptive governance: an analysis of tools available in U.S. environmental law.

Adaptive governance must work "on the ground," that is, it must operate through structures and procedures that the people it governs perceive to be legitimate and fair, as well as incorporating processes and substantive goals that are effective in allowing social-ecological systems (SESs) to adapt to climate change and other impacts. To address the continuing and accelerating alterations that climate change is bringing to SESs, adaptive governance generally will require more flexibility than prior governance institutions have often allowed. However, to function as good governance, adaptive governance must pay real attention to the problem of how to balance this increased need for flexibility with continuing governance stability so that it can foster adaptation to change without being perceived or experienced as perpetually destabilizing, disruptive, and unfair. Flexibility and stability serve different purposes in governance, and a variety of tools exist to strike different balances between them while still preserving the governance institution's legitimacy among the people governed. After reviewing those purposes and the implications of climate change for environmental governance, we examine psychological insights into the structuring of adaptive governance and the variety of legal tools available to incorporate those insights into adaptive governance regimes. Because the substantive goals of governance systems will differ among specific systems, we do not purport to comment on what the normative or substantive goals of law should be. Instead, we conclude that attention to process and procedure (including participation), as well as increased use of substantive standards (instead of rules), may allow an increased level of substantive flexibility to operate with legitimacy and fairness, providing the requisite levels of psychological, social, and economic stability needed for communities to adapt successfully to the Anthropocene.

Scaling up functional traits for ecosystem services with remote sensing: concepts and methods.

Ecosystem service-based management requires an accurate understanding of how human modification influences ecosystem processes and these relationships are most accurate when based on functional traits. Although trait variation is typically sampled at local scales, remote sensing methods can facilitate scaling up trait variation to regional scales needed for ecosystem service management. We review concepts and methods for scaling up plant and animal functional traits from local to regional spatial scales with the goal of assessing impacts of human modification on ecosystem processes and services. We focus our objectives on considerations and approaches for (1) conducting local plot-level sampling of trait variation and (2) scaling up trait variation to regional spatial scales using remotely sensed data. We show that sampling methods for scaling up traits need to account for the modification of trait variation due to land cover change and species introductions. Sampling intraspecific variation, stratification by land cover type or landscape context, or inference of traits from published sources may be necessary depending on the traits of interest. Passive and active remote sensing are useful for mapping plant phenological, chemical, and structural traits. Combining these methods can significantly improve their capacity for mapping plant trait variation. These methods can also be used to map landscape and vegetation structure in order to infer animal trait variation. Due to high context dependency, relationships between trait variation and remotely sensed data are not directly transferable across regions. We end our review with a brief synthesis of issues to consider and outlook for the development of these approaches. Research that relates typical functional trait metrics, such as the community-weighted mean, with remote sensing data and that relates variation in traits that cannot be remotely sensed to other proxies is needed. Our review narrows the gap between functional trait and remote sensing methods for ecosystem service management.

Quantifying process-based mitigation strategies in historical context: separating multiple cumulative effects on river meander migration.

Environmental legislation in the US (i.e. NEPA) requires defining baseline conditions on current rather than historical ecosystem conditions. For ecosystems with long histories of multiple environmental impacts, this baseline method can subsequently lead to a significantly altered environment; this has been termed a 'sliding baseline'. In river systems, cumulative effects caused by flow regulation, channel revetment and riparian vegetation removal significantly impact floodplain ecosystems by altering channel dynamics and precluding subsequent ecosystem processes, such as primary succession. To quantify these impacts on floodplain development processes, we used a model of river channel meander migration to illustrate the degree to which flow regulation and riprap impact migration rates, independently and synergistically, on the Sacramento River in California, USA. From pre-dam conditions, the cumulative effect of flow regulation alone on channel migration is a reduction by 38%, and 42-44% with four proposed water diversion project scenarios. In terms of depositional area, the proposed water project would reduce channel migration 51-71 ha in 130 years without current riprap in place, and 17-25 ha with riprap. Our results illustrate the utility of a modeling approach for quantifying cumulative impacts. Model-based quantification of environmental impacts allow scientists to separate cumulative and synergistic effects to analytically define mitigation measures. Additionally, by selecting an ecosystem process that is affected by multiple impacts, it is possible to consider process-based mitigation scenarios, such as the removal of riprap, to allow meander migration and create new floodplains and allow for riparian vegetation recruitment.

The ectomycorrhizal fungal community in a neotropical forest dominated by the endemic dipterocarp Pakaraimaea dipterocarpacea.

Ectomycorrhizal (ECM) plants and fungi can be diverse and abundant in certain tropical ecosystems. For example, the primarily paleotropical ECM plant family Dipterocarpaceae is one of the most speciose and ecologically important tree families in Southeast Asia. Pakaraimaea dipterocarpacea is one of two species of dipterocarp known from the Neotropics, and is also the only known member of the monotypic Dipterocarpaceae subfamily Pakaraimoideae. This Guiana Shield endemic is only known from the sandstone highlands of Guyana and Venezuela. Despite its unique phylogenetic position and unusual geographical distribution, the ECM fungal associations of P. dipterocarpacea are understudied throughout the tree's range. In December 2010 we sampled ECM fungi on roots of P. dipterocarpacea and the co-occurring ECM tree Dicymbe jenmanii (Fabaceae subfamily Caesalpinioideae) in the Upper Mazaruni River Basin of Guyana. Based on ITS rDNA sequencing we documented 52 ECM species from 11 independent fungal lineages. Due to the phylogenetic distance between the two host tree species, we hypothesized that P. dipterocarpacea would harbor unique ECM fungi not found on the roots of D. jenmanii. Although statistical tests suggested that several ECM fungal species did exhibit host preferences for either P. dipterocarpacea or D. jenmanii, most of the ECM fungi were multi-host generalists. We also detected several ECM fungi that have never been found in long-term studies of nearby rainforests dominated by other Dicymbe species. One particular mushroom-forming fungus appears to be unique and may represent a new ECM lineage of Agaricales that is endemic to the Neotropics.

Global sensitivity analysis for complex ecological models: a case study of riparian cottonwood population dynamics.

Mechanism-based ecological models are a valuable tool for understanding the drivers of complex ecological systems and for making informed resource-management decisions. However, inaccurate conclusions can be drawn from models with a large degree of uncertainty around multiple parameter estimates if uncertainty is ignored. This is especially true in nonlinear systems with multiple interacting variables. We addressed these issues for a mechanism-based, demographic model of Populus fremontii (Fremont cottonwood), the dominant riparian tree species along southwestern U.S. rivers. Many cottonwood populations have declined following widespread floodplain conversion and flow regulation. As a result, accurate predictive models are needed to analyze effects of future climate change and water management decisions. To quantify effects of parameter uncertainty, we developed an analytical approach that combines global sensitivity analysis (GSA) with classification and regression trees (CART) and Random Forest, a bootstrapping CART method. We used GSA to quantify the interacting effects of the full range of uncertainty around all parameter estimates, Random Forest to rank parameters according to their total effect on model predictions, and CART to identify higher-order interactions. GSA simulations yielded a wide range of predictions, including annual germination frequency of 10-100%, annual first-year survival frequency of 0-50%, and patch occupancy of 0-100%. This variance was explained primarily by complex interactions among abiotic parameters including capillary fringe height, stage-discharge relationship, and floodplain accretion rate, which interacted with biotic factors to affect survival. Model precision was primarily influenced by well-studied parameter estimates with minimal associated uncertainty and was virtually unaffected by parameter estimates for which there are no available empirical data and thus a large degree of uncertainty. Therefore, research to improve model predictions should not always focus on the least-studied parameters, but rather those to which model predictions are most sensitive. We advocate the combined use of global sensitivity analysis, CART, and Random Forest to: (1) prioritize research efforts by ranking variable importance; (2) efficiently improve models by focusing on the most important parameters; and (3) illuminate complex model properties including nonlinear interactions. We present an analytical framework that can be applied to any model with multiple uncertain parameter estimates.

Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time.

Quantifying the influence of the landscape on the genetic structure of natural populations remains an important empirical challenge, particularly for poorly studied, ecologically cryptic species. We conducted an extensive microsatellite analysis to examine the population genetics of the southern long-toed salamander (Ambystoma macrodactylum sigillatum) in a naturally complex landscape. Using spatially explicit modelling, we investigated the influence of the Sierra Nevada topography on potential dispersal corridors between sampled populations. Our results indicate very high-genetic divergence among populations, high within-deme relatedness, and little evidence of recent migration or population admixture. We also discovered unexpectedly high between-year genetic differentiation (F(ST)) for breeding sites, suggesting that breeding groups vary over localized space and time. While environmental factors associated with high-elevation montane habitats apparently play an important role in shaping population differentiation, additional, species-specific biological processes must also be operating to account for observed deviations from temporal, among-year panmixia. Our study emphasizes the population-level insights that can be gained from high-density sampling in space and time, and the highly substructured population biology that may characterize amphibians in extreme montane habitats.

Understanding the ecology of blue elderberry to inform landscape restoration in semiarid river corridors.

Societal constraints often limit full process restoration in large river systems, making local rehabilitation activities valuable for regeneration of riparian vegetation. A target of much mitigation and restoration is the federally threatened Valley elderberry longhorn beetle and its sole host plant, blue elderberry, in upper riparian floodplain environments. However, blue elderberry ecology is not well understood and restoration attempts typically have low success rates. We determined broad-scale habitat characteristics of elderberry in altered systems and examined associated plant species composition in remnant habitat. We quantified vegetation community composition in 139 remnant riparian forest patches along the Sacramento River and elderberry stem diameters along this and four adjacent rivers. The greatest proportion of plots containing elderberry was located on higher and older floodplain surfaces and in riparian woodlands dominated by black walnut. Blue elderberry saplings and shrubs with stems <5.0 cm in diameter were rare, suggesting a lack of recruitment. A complex suite of vegetation was associated with blue elderberry, including several invasive species which are potentially outcompeting seedlings for light, water, or other resources. Such lack of recruitment places increased importance on horticultural restoration for the survival of an imperiled species. These findings further indicate a need to ascertain whether intervention is necessary to maintain functional and diverse riparian woodlands, and a need to monitor vegetative species composition over time, especially in relation to flow regulation.

Assessing the effects of alternative setback channel constraint scenarios employing a river meander migration model.

River channel migration and cutoff events within large river riparian corridors create heterogeneous and biologically diverse landscapes. However, channel stabilization (riprap and levees) impede the formation and maintenance of riparian areas. These impacts can be mitigated by setting channel constraints away from the channel. Using a meander migration model to measure land affected, we examined the relationship between setback distance and riparian and off-channel aquatic habitat formation on a 28-km reach of the Sacramento River, California, USA. We simulated 100 years of channel migration and cutoff events using 11 setback scenarios: 1 with existing riprap and 10 assuming setback constraints from about 0.5 to 4 bankfull channel widths (bankfull width: 235 m) from the channel. The percentage of land reworked by the river in 100 years relative to current (riprap) conditions ranged from 172% for the 100-m constraint setback scenario to 790% for the 800-m scenario. Three basic patterns occur as the setback distance increases due to different migration and cutoff dynamics: complete restriction of cutoffs, partial restriction of cutoffs, and no restriction of cutoffs. Complete cutoff restriction occurred at distances less than about one bankfull channel width (235 m), and no cutoff restriction occurred at distances greater than about three bankfull widths (approximately 700 m). Managing for point bars alone allows the setbacks to be narrower than managing for cutoffs and aquatic habitat. Results suggest that site-specific "restriction of cutoff" thresholds can be identified to optimize habitat benefits versus cost of acquired land along rivers affected by migration processes.