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USGS2017

Short-term ecological consequences of collaborative restoration treatments in ponderosa pine forests of Colorado

Ecological restoration treatments are being implemented at an increasing rate in ponderosa pine and other dry conifer forests across the western United States, via the USDA Forest Service’s Collaborative Forest Landscape Restoration (CFLR) program. In this program, collaborative stakeholder groups work with National Forests (NFs) to adaptively implement and monitor ecological restoration treatments intended to offset the effects of many decades of anthropogenic stressors. We initiated a novel study to expand the scope of treatment effectiveness monitoring efforts in one of the first CFLR landscapes, Colorado’s Front Range. We used a Before/After/Control/Impact framework to evaluate the short-term consequences of treatments on numerous ecological properties. We collected pre-treatment and one year post-treatment data on NF and partner agencies’ lands, in 66 plots distributed across seven treatment units and nearby untreated areas. Our results reflected progress toward several treatment objectives: treated areas had lower tree density and basal area, greater openness, no increase in exotic understory plants, no decrease in native understory plants, and no decrease in use by tree squirrels and ungulates. However, some findings suggested the need for adaptive modification of both treatment prescriptions and monitoring protocols: treatments did not promote heterogeneity of stand structure, and monitoring methods may not have been robust enough to detect changes in surface fuels. Our study highlights both the effective aspects of these restoration treatments, and the importance of initiating and continuing collaborative science-based monitoring to improve the outcomes of broad-scale forest restoration efforts.

Colorado↗

USGS2021

Assessing the ecological functionality and integrity of natural ponds, excavated ponds and stormwater basins for conserving amphibian diversity

Wetlands provide ecological functionality by maintaining and promoting regional biodiversity supporting quality habitat for aquatic organisms. Globally, habitat loss, fragmentation and degradation due to increases in agricultural activities and urban development have reduced or altered geographically isolated wetlands, thus reducing biodiversity. The objective of this study was to assess the relative ecological function and integrity of natural ponds, excavated ponds and stormwater basins in the New Jersey Pinelands, located in the northeastern United States by comparing hydrologic conditions, water quality, pesticide concentrations (water, sediment and tissue) and wetland assemblages including amphibians. Twenty-four wetlands were selected based on surrounding land-use and sampled for a variety of abiotic and biotic variables. Abiotic and biotic wetland variables were similar between natural and excavated ponds, with notable differences between the ponds and stormwater basins. Natural and excavated ponds displayed characteristic Pinelands water quality (low pH, high organic carbon, and low pesticide concentrations), exhibited high ecological integrity and supported native ampbibians. Stormwater basins and degraded ponds surrounded by altered land-use exhibited degraded water quality (high pH, high pesticide concentrations) and were dominated by non-native and introduced plants and amphibians. Results from this study can broadly inform resource conservation strategies for amphibians and other communities with a diverse range of habitat requirements, particularly in areas where conservation and development are competing priorities. To conserve biodiversity in changing landscapes, wetlands with similar functionality and land-use characteristics need to be identified and managed to preserve water quality for species of conservation concern.

New Jersey↗

USGS2021

Hawai‘i forest review: Synthesizing the ecology, evolution, and conservation of a model system

As the most remote archipelago in the world, the Hawaiian Islands are home to a highly endemic and disharmonic biota that has fascinated biologists for centuries. Forests are the dominant terrestrial biome in Hawai‘i, spanning complex, heterogeneous climates across substrates that vary tremendously in age, soil structure, and nutrient availability. Species richness is low in Hawaiian forests compared to other tropical forests, as a consequence of dispersal limitation from continents and adaptive radiations in only some lineages, and forests are dominated by the widespread Metrosideros species complex. Low species richness provides a relatively tractable model system for studies of community assembly, local adaptation, and species interactions. Moreover, Hawaiian forests provide insights into predicted patterns of evolution on islands, revealing that while some evidence supports “island syndromes,” there are exceptions to them all. For example, Hawaiian plants are not as a whole less defended against herbivores, less dispersible, more conservative in resource use, or more slow-growing than their continental relatives. Clearly, more work is needed to understand the drivers, sources, and constraints on phenotypic variation among Hawaiian species, including both widespread and rare species, and to understand the role of this variation for ecological and evolutionary processes, which will further contribute to conservation of this unique biota. Today, Hawaiian forests are among the most threatened globally. Resource management failures – the proliferation of non-native species in particular – have led to devastating declines in native taxa and resulted in dominance by novel species assemblages. Conservation and restoration of Hawaiian forests now rely on managing threats including climate change, ongoing species introductions, novel pathogens, lost mutualists, and altered ecosystem dynamics through the use of diverse tools and strategies grounded in basic ecological, evolutionary, and biocultural principles. The future of Hawaiian forests thus depends on the synthesis of ecological and evolutionary research, which will continue to inform future conservation and restoration practices.

Hawaii↗

USGS2020

Departures of rangeland fractional component cover and land cover from landsat-based ecological potential in Wyoming USA

Monitoring rangelands by identifying the departure of contemporary conditions from long-term ecological potential allows for the disentanglement of natural biophysical gradients driving change from changes associated with land uses and other disturbance types. We developed maps of ecological potential (EP) for shrub, sagebrush ( Artemisia spp.), perennial herbaceous, litter, and bare ground fractional cover in Wyoming, USA. EP maps correspond to the potential natural vegetation cover expected by environmental conditions in the absence of anthropogenic and natural disturbance as represented by the greenest and least disturbed period of the Landsat archive. EP was predicted using regression tree models with inputs of soil maps and spectral data associated with the 75th percentile of the Normalized Difference Vegetation Index in the Landsat archive. We trained our EP models with 2015 component cover maps on ecologically intact sites with relatively lower bare ground than expected. We generated departure of vegetation cover by comparing the EP and 2015 fractional cover. The departures represent land cover change from potential land cover and/or within-state changes in 2015. Next, we converted EP and 2015 fractional cover maps into thematic land cover and evaluated departure to determine if it was great enough to result in land cover change. The 2015 conditions showed reduced shrub, sagebrush, litter, and perennial herbaceous cover and increased bare ground relative to EP. Known disturbances, such as energy development, fires, and vegetation treatments, are clearly visible on the departure maps, but not on EP component maps. The most frequent departure from EP land cover was shrubland conversion to grassland. Land cover departures can be explained only in small part by known disturbance, and instead are ostensibly related to climate and land management practices. These drivers result in land cover departures that broadened the ecotone between shrubland and grassland relative to EP.

Wyoming↗

USGS2023

Climate change and coastal wetland salinization: Physiological and ecological consequences for Arctic waterfowl

Coastal wetland salinization related to warming climate has the potential to impact ecological systems globally. In Alaska, the Yukon-Kuskokwim Delta (YKD) supports large concentrations of breeding water birds and is an ecologically important area for conservation of migratory bird biodiversity. On the YKD, the majority of waterfowl nest in low elevation coastal tundra where storm surges drive saline water into terrestrial wetland habitats. Because newly hatched water birds lack functional salt glands to process saline water, salinization may negatively impact their growth and survival. We investigated potential demographic impacts of wetland salinization by conducting controlled physiological experiments to determine consequences of saline water exposure to spectacled Somateria fischeri and Steller's eider Polysticta stelleri ducklings, and analysed habitat suitability based on experimentally defined tolerance thresholds and sampled wetland salinity levels. We found physiological and behavioural pathologies in <1 week old ducklings at exposure levels of 6 parts per thousand (ppt), and found some evidence of reduced growth in ducklings first exposed after 1 week of age. We conclude that the acute toxicity threshold for ducklings <1 week of age is ≤6 ppt. We found that the area of coastal tundra where wetland salinity exceeded 6 ppt varied considerably among years, suggesting that some portion of the breeding range is unsuitable for rearing ducklings in some years. However, we also found that most eiders in most years nested in areas with salinity at or exceeding the tolerance threshold for ducklings, suggesting that nesting eiders do not appear to avoid saline habitats. We suggest that localized fresh water refugia currently may allow resilience to salinization during the critical period. Understanding how species and habitats respond to climate driven changes is essential for predicting future patterns of distribution and abundance, and is necessary for making informed decisions about conservation priorities. Our study provides insights into the extent of wetland salinization in Alaska, mechanism of impact and current ecological consequences on avian communities depending on these habitats. With ongoing climate change, the probability of species crossing physiological tolerance thresholds of wetland salinity may change in the future.

Functional Ecology↗

USGS2015

FORUM: Effective management of ecological resilience – are we there yet?

Ecological resilience is developing into a credible paradigm for policy development and environmental management for preserving natural capital in a rapidly changing world. However, resilience emerges from complex interactions, limiting the translation of theory into practice. Main limitations include the following: (i) difficulty in quantification and detection of changes in ecological resilience, (ii) a lack of empirical evidence to support preventative or proactive management and (iii) difficulties in managing processes operating across socio-ecological systems that vary in space and time. We highlight recent research with the potential to address these limitations including new and/or improved indicators of resilience and tools to assess scale as a driver of resilience. Synthesis and applications . Effective resilience-based management must be adaptive in nature. To support this, we propose an operational model using resilience-based iterative management actions operating across scales.

Journal of Applied Ecology↗

USGS2018

DNA mixtures for ecology

Mixtures of DNA from multiple contributors present a novel opportunity to count individuals to inform fish and wildlife ecology. We apply a likelihood-based framework to estimate the number of contributors to a DNA mixture for ecological applications. We then assess the performance of DNA mixture estimation through a combination of simulation analyses, laboratory testing, and a field trial to estimate fish predation rates from stomach content analysis. Simulations indicated reasonably sized genetic marker panels could estimate the number of contributors to mixtures comprised of up to 10 individuals, with potential to resolve larger mixtures with additional markers. Mixture estimates demonstrated robustness to common genotyping errors associated with fish and wildlife genetics applications. Laboratory trials demonstrated that DNA combined from multiple yellow perch ( Perca flavescens ) could be successfully genotyped with a 14-loci microsatellite panel and led to successful estimation for up to 5-contributor mixtures. Stomach content analysis with DNA mixtures indicated a 5-fold increase in estimated predation rates of yellow perch by largemouth bass ( Micropterus salmoides ) relative to conventional visual assessment of diet contents which can miss partially digested prey items. DNA mixtures have potential to expand applications of count-based ecological analyses. Technical challenges in generating genotypes from DNA mixtures may initially limit their use, however, advances in next generation genotyping platforms are anticipated to surmount these obstacles. Chiefly, we envision opportunity for DNA mixtures to advance eDNA analysis beyond presence/absence based inference to enumeration of specimens.

Methods in Ecology and Evolution↗

USGS2019

Sampling and analysis frameworks for inference in ecology

1. Reliable statistical inference is central to ecological research, much of which seeks to estimate population attributes and their interactions. The issue of sampling design and its relationship to inference has become increasingly important due to rapid proliferation of modeling methodology (line transect modeling, capture-recapture, estimation of occurrence, model selection procedures, hierarchical modeling) and new sampling approaches (adaptive sampling, other specialized designs). It is important for ecologists using these advanced methods to be aware of how the linkages between sample selection and data analysis can potentially affect inference. 2. We examine design-based and model-based inference frameworks for ecological data collected randomly, purposively, or opportunistically. We elucidate differences in the probability structures for data arising from these frameworks, clarify the assumptions that underlie them, and demonstrate their differences. 3. Design-based inference builds on a probability structure inherited from randomized data collection, whereas model-based inference relies on an assumed stochastic model of the data. By itself, a design-based approach is of limited value for inferences about causal hypotheses. In contrast, model-based inference is dependent on a conditionality principle that can seldom be shown to be met for an ecological system. We describe the conditions under which one can safely ignore sampling design in model-based analysis, along with inferential implications if these conditions are not met. The special case of opportunistic sampling is discussed. 4. We present a combined framework that takes advantage of both approaches to inference, and provides a robust methodology that can deal with the modeling of sampling problems such as nondetection and misclassification, as well as the exploration of causal hypotheses. The combined framework can be useful for identifying optimal sampling strategies. 5. Each approach to inference has its strengths and weaknesses, and practitioners should be aware of these in order to tailor designs and analyses to specific questions. We use the approaches and their underlying rationales to provide guidelines for choosing designs and estimators for reliable inference.

Methods in Ecology and Evolution↗

USGS2023

Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses

1. Integrating ecological theory with empirical methods is ubiquitous in ecology using hierarchical Bayesian models. However, there has been little development focused on integration of ecological theory into models for survival analysis. Survival is a fundamental process, linking individual fitness with population dynamics, but incorporating life history strategies to inform survival estimation can be challenging because mortality processes occur at multiple scales. 2. We develop an approach to survival analysis, incorporating model constraints based on a species' life history strategy using functional analytical tools. Specifically, we structurally separate intrinsic patterns of mortality that arise from age-specific processes (e.g. increasing survival during early life stages due to growth or maturation, versus senescence) from extrinsic mortality patterns that arise over different periods of time (e.g. seasonal temporal shifts). We use shape constrained generalized additive models (CGAMs) to obtain age-specific hazard functions that incorporate theoretical information based on classical survivorship curves into the age component of the model and capture extrinsic factors in the time component. 3. We compare the performance of our modelling approach to standard survival modelling tools that do not explicitly incorporate species life history strategy in the model structure, using metrics of predictive power, accuracy, efficiency and computation time. We applied these models to two case studies that reflect different functional shapes for the underlying survivorship curves, examining age-period survival for white-tailed deer Odocoileus virginianus in Wisconsin, USA and Columbian sharp-tailed grouse T ympanuchus phasianellus columbianus in Colorado, USA.

Colorado, Wisconsin↗

USGS2011

Stopover ecology of a migratory ungulate

1. Birds that migrate long distances use stopover sites to optimize fuel loads and complete migration as quickly as possible. Stopover use has been predicted to facilitate a time-minimization strategy in land migrants as well, but empirical tests have been lacking, and alternative migration strategies have not been considered. 2. We used fine-scale movement data to evaluate the ecological role of stopovers in migratory mule deer Odocoileus hemionus — a land migrant whose fitness is strongly influenced by energy intake rather than migration speed. 3. Although deer could easily complete migrations (range 18–144 km) in several days, they took an average of 3 weeks and spent 95% of that time in a series of stopover sites that had higher forage quality than movement corridors. Forage quality of stopovers increased with elevation and distance from winter range. Mule deer use of stopovers corresponded with a narrow phenological range, such that deer occupied stopovers 44 days prior to peak green-up, when forage quality was presumed to be highest. Mule deer used one stopover for every 5∙3 and 6∙7 km travelled during spring and autumn migrations, respectively, and used the same stopovers in consecutive years. 4. Study findings indicate that stopovers play a key role in the migration strategy of mule deer by allowing individuals to migrate in concert with plant phenology and maximize energy intake rather than speed. Our results suggest that stopover use may be more common among non-avian taxa than previously thought and, although the underlying migration strategies of temperate ungulates and birds are quite different, stopover use is important to both. 5. Exploring the role of stopovers in land migrants broadens the scope of stopover ecology and recognizes that the applied and theoretical benefits of stopover ecology need not be limited to avian taxa.

Journal of Animal Ecology↗

USGS2018

Monitoring the social benefits of ecological restoration

Ecological restoration has traditionally been evaluated by monitoring the recovery of ecosystem conditions, such as species diversity and abundance, physical form, and water quality, whereas monitoring the social benefits of restoration is uncommon. Current monitoring frameworks do not track who benefits from restoration or by how much. In this study, we investigate how ecological restoration could be monitored to provide indications of progress in terms of social conditions. We provide suggestions for measuring several categories of benefit indicators, including access, beneficiaries, and quality of benefit, using information compiled from natural and social science literature. We also demonstrate how to evaluate ecological and social benefit indicators over time at a site or landscape scale using multi-criteria analysis. We use flood protection and recreation as example benefits to monitor.

Restoration Ecology↗

USGS2005

Individual-based modeling of ecological and evolutionary processes

Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.

Annual Review of Ecology, Evolution, and Systemati↗

USGS2007

Random forests for classification in ecology

Classification procedures are some of the most widely used statistical methods in ecology. Random forests (RF) is a new and powerful statistical classifier that is well established in other disciplines but is relatively unknown in ecology. Advantages of RF compared to other statistical classifiers include (1) very high classification accuracy; (2) a novel method of determining variable importance; (3) ability to model complex interactions among predictor variables; (4) flexibility to perform several types of statistical data analysis, including regression, classification, survival analysis, and unsupervised learning; and (5) an algorithm for imputing missing values. We compared the accuracies of RF and four other commonly used statistical classifiers using data on invasive plant species presence in Lava Beds National Monument, California, USA, rare lichen species presence in the Pacific Northwest, USA, and nest sites for cavity nesting birds in the Uinta Mountains, Utah, USA. We observed high classification accuracy in all applications as measured by cross-validation and, in the case of the lichen data, by independent test data, when comparing RF to other common classification methods. We also observed that the variables that RF identified as most important for classifying invasive plant species coincided with expectations based on the literature. ?? 2007 by the Ecological Society of America.

Ecology↗

USGS2010

Predicting performance for ecological restoration: A case study using Spartina altemiflora

The success of population-based ecological restoration relies on the growth and reproductive performance of selected donor materials, whether consisting of whole plants or seed. Accurately predicting performance requires an understanding of a variety of underlying processes, particularly gene flow and selection, which can be measured, at least in part, using surrogates such as neutral marker genetic distances and simple latitudinal effects. Here we apply a structural equation modeling approach to understanding and predicting performance in a widespread salt marsh grass, Spartina alterniflora, commonly used for ecological restoration throughout its native range in North America. We collected source materials from throughout this range, consisting of eight clones each from 23 populations, for transplantation to a common garden site in coastal Louisiana and monitored their performance. We modeled performance as a latent process described by multiple indicator variables (e.g., clone diameter, stem number) and estimated direct and indirect influences of geographic and genetic distances on performance. Genetic distances were determined by comparison of neutral molecular markers with those from a local population at the common garden site. Geographic distance metrics included dispersal distance (the minimum distance over water between donor and experimental sites) and latitude. Model results indicate direct effects of genetic distance and latitude on performance variation among the donor sites. Standardized effect strengths indicate that performance was roughly twice as sensitive to variation in genetic distance as to latitudinal variation. Dispersal distance had an indirect influence on performance through effects on genetic distance, indicating a typical pattern of genetic isolation by distance. Latitude also had an indirect effect on genetic distance through its linear relationship with dispersal distance. Three performance indicators had significant loadings on performance alone (mean clone diameter, mean number of stems, mean number of inflorescences), while the performance indicators mean stem height and mean stem width were also influenced by latitude. We suggest that dispersal distance and latitude should provide an adequate means of predicting performance in future S. alterniflora restorations and propose a maximum sampling distance of 300 km (holding latitude constant) to avoid the sampling of inappropriate ecotypes. ?? 2010 by the Ecological Society of America.

Ecological Applications↗

USGS2010

On the specification of structural equation models for ecological systems

The use of structural equation modeling (SEM) is often motivated by its utility for investigating complex networks of relationships, but also because of its promise as a means of representing theoretical concepts using latent variables. In this paper, we discuss characteristics of ecological theory and some of the challenges for proper specification of theoretical ideas in structural equation models (SE models). In our presentation, we describe some of the requirements for classical latent variable models in which observed variables (indicators) are interpreted as the effects of underlying causes. We also describe alternative model specifications in which indicators are interpreted as having causal influences on the theoretical concepts. We suggest that this latter nonclassical specification (which involves another variable type—the composite) will often be appropriate for ecological studies because of the multifaceted nature of our theoretical concepts. In this paper, we employ the use of meta‐models to aid the translation of theory into SE models and also to facilitate our ability to relate results back to our theories. We demonstrate our approach by showing how a synthetic theory of grassland biodiversity can be evaluated using SEM and data from a coastal grassland. In this example, the theory focuses on the responses of species richness to abiotic stress and disturbance, both directly and through intervening effects on community biomass. Models examined include both those based on classical forms (where each concept is represented using a single latent variable) and also ones in which the concepts are recognized to be multifaceted and modeled as such. To address the challenge of matching SE models with the conceptual level of our theory, two approaches are illustrated, compositing and aggregation. Both approaches are shown to have merits, with the former being preferable for cases where the multiple facets of a concept have widely differing effects in the system and the latter being preferable where facets act together consistently when influencing other parts of the system. Because ecological theory characteristically deals with concepts that are multifaceted, we expect the methods presented in this paper will be useful for ecologists wishing to use SEM.

Ecological Monographs↗

USGS2003

Ecological criteria for evaluating candidate sites for marine reserves

Several schemes have been developed to help select the locations of marine reserves. All of them combine social, economic, and biological criteria, and few offer any guidance as to how to prioritize among the criteria identified. This can imply that the relative weights given to different criteria are unimportant. Where two sites are of equal value ecologically, then socioeconomic criteria should dominate the choice of which should be protected. However, in many cases, socioeconomic criteria are given equal or greater weight than ecological considerations in the choice of sites. This can lead to selection of reserves with little biological value that fail to meet many of the desired objectives. To avoid such a possibility, we develop a series of criteria that allow preliminary evaluation of candidate sites according to their relative biological values in advance of the application of socioeconomic criteria. We include criteria that, while not strictly biological, have a strong influence on the species present or ecological processes. Our scheme enables sites to be assessed according to their biodiversity, the processes which underpin that diversity, and the processes that support fisheries and provide a spectrum of other services important to people. Criteria that capture biodiversity values include biogeographic representation, habitat representation and heterogeneity, and presence of species or populations of special interest (e.g., threatened species). Criteria that capture sustainability of biodiversity and fishery values include the size of reserves necessary to protect viable habitats, presence of exploitable species, vulnerable life stages, connectivity among reserves, links among ecosystems, and provision of ecosystem services to people. Criteria measuring human and natural threats enable candidate sites to be eliminated from consideration if risks are too great, but also help prioritize among sites where threats can be mitigated by protection. While our criteria can be applied to the design of reserve networks, they also enable choice of single reserves to be made in the context of the attributes of existing protected areas. The overall goal of our scheme is to promote the development of reserve networks that will maintain biodiversity and ecosystem functioning at large scales. The values of ecosystem goods and services for people ultimately depend on meeting this objective.

Ecological Applications↗

USGS2015

Legacy effects in linked ecological-soil-geomorphic systems of drylands

A legacy effect refers to the impacts that previous conditions have on current processes or properties. Legacies have been recognized by many disciplines, from physiology and ecology to anthropology and geology. Within the context of climatic change, ecological legacies in drylands (eg vegetative patterns) result from feedbacks between biotic, soil, and geomorphic processes that operate at multiple spatial and temporal scales. Legacy effects depend on (1) the magnitude of the original phenomenon, (2) the time since the occurrence of the phenomenon, and (3) the sensitivity of the ecological–soil–geomorphic system to change. Here we present a conceptual framework for legacy effects at short-term (days to months), medium-term (years to decades), and long-term (centuries to millennia) timescales, which reveals the ubiquity of such effects in drylands across research disciplines.

Frontiers in Ecology and the Environment↗

USGS2007

New ecological knowledge and practices for society and sustainability

As attributes of the Earth's ecosystems shift in the face of human impact and sustainability of ecosystem services becomes less certain, one important tool at the disposal of the scientific community and other groups is a blueprint for understanding, evaluating, and communicating the value of ecological services. The blueprint presented here is based on (1) an examination of the ecological and societal trade-offs accompanying any given action, (2) revised methods of communication, and (3) coordination of actions at many different scales. The Mexican National Commission for the Knowledge and Use of Biodiversity (CONABIO) is a good example of a demand-driven “bridging institution” between academia, government, and civil society, and it works to collect and convert scientific information into information for policy, management, and conservation. Intergovernmental organizations like the United Nations Educational, Scientific and Cultural Organization (UNESCO) are well placed to facilitate such coordination at the international level, through their work with member states. Through collaboration with the constituencies of such organizations as the Ecological Society of America, the blueprint described below has the potential to become an important tool for assessing and managing threats to ecosystem services that are essential to life.

Frontiers in Ecology and the Environment↗