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USGS2001

Mapping wildland fuels for fire management across multiple scales: integrating remote sensing, GIS, and biophysical modeling

Fuel maps are essential for computing spatial fire hazard and risk and simulating fire growth and intensity across a landscape. However, fuel mapping is an extremely difficult and complex process requiring expertise in remotely sensed image classification, fire behavior, fuels modeling, ecology, and geographical information systems (GIS). This paper first presents the challenges of mapping fuels: canopy concealment, fuelbed complexity, fuel type diversity, fuel variability, and fuel model generalization. Then, four approaches to mapping fuels are discussed with examples provided from the literature: (1) field reconnaissance; (2) direct mapping methods; (3) indirect mapping methods; and (4) gradient modeling. A fuel mapping method is proposed that uses current remote sensing and image processing technology. Future fuel mapping needs are also discussed which include better field data and fuel models, accurate GIS reference layers, improved satellite imagery, and comprehensive ecosystem models.

International Journal of Wildland Fire↗

USGS2017

Ecological impacts of winter water level drawdowns on lake littoral zones: A review

Freshwater littoral zones harbor diverse ecological communities and serve numerous ecosystem functions that are controlled, in part, by natural water level fluctuations. However, human alteration of lake hydrologic regimes beyond natural fluctuations threaten littoral zone ecological integrity. One type of hydrologic alteration in lakes is winter water level drawdowns, which are frequently employed for hydropower, flood control, and macrophyte control, among other purposes. Here, we synthesize the abiotic and biotic responses to annual and novel winter water level drawdowns in littoral zones of lakes and reservoirs. The dewatering, freezing, and increased erosion of exposed lakebeds drive changes in the littoral zone. Shoreline-specific physicochemical conditions such as littoral slope and shoreline exposure further induce modifications. Loss of fine sediment decreases nutrient availability over time, but desiccation may promote a temporary nutrient pulse upon re-inundation. Annual winter drawdowns can decrease taxonomic richness of macrophytes and benthic invertebrates and shift assemblage composition to favor taxa with r-selected life history strategies and with functional traits resistant to direct and indirect drawdown effects. Fish assemblages, though less directly affected by winter drawdowns (except where there is critically low dissolved oxygen), experience negative effects via indirect pathways like decreased food resources and spawning habitat. We identify eight general research gaps to guide future research that could improve our understanding about the complex effects of winter drawdowns on littoral zone ecology.

Aquatic Sciences↗

USGS2022

Urbanization and stream ecology: Moving the bar on multidisciplinary solutions to wicked urban stream problems

Decades of research on the effects of urbanization on stream ecology have shown that urban stream problems are inherently wicked. These problems are wicked in the sense that they are difficult to solve because information is incomplete, changing, or conflicting and because finding potential solutions often requires input from stakeholders who can have conflicting and competing values. The 5 th Symposium on Urbanization and Stream Ecology (SUSE5) in February 2020 brought together diverse perspectives from scientists, managers, practitioners, and local communities. Participants at SUSE5 discussed the state of the science in urban stream ecology and worked through in-depth case studies in teams to tackle complex real-world problems in urban stream management. The papers in this special series on urbanization and stream ecology include empirical research studies and synthesis papers sparked by discussions at SUSE5 and advance multidisciplinary solutions to wicked urban stream problems.

Freshwater Science↗

USGS2022

Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae: Coregonus spp.)

Groups of sympatric taxa with low interspecific genetic differentiation, but considerable ecological differences, offer great opportunities to study the dynamics of divergence and speciation. This is the case of ciscoes ( Coregonus spp.) in the Laurentian Great Lakes, which are characterized by a complex evolutionary history and are commonly described as having undergone an adaptive radiation. In this study, morphometrics, stable isotopes and transcriptome sequencing were used to study the relationships within the Coregonus artedi complex in western Lake Superior. We observed general concordance for morphological, ecological and genomic variation, but the last was more taxonomically informative as it showed less overlap among species in multivariate space. Low levels of genetic differentiation were observed between individuals morphologically identified as Coregonus hoyi and C. zenithicus , which could be evidence of incomplete lineage sorting or recent hybridization between the two groups. Transcriptome-based single nucleotide polymorphisms exhibited significant divergence for genes associated with vision, development, metabolism and immunity among species that occupy different habitats. This study highlights the importance of using an integrative approach when studying groups of taxa with a complex evolutionary history, as individual-level analyses of multiple independent data sets can provide a clearer picture of the patterns and processes associated with the origins of biodiversity.

Michigan, Minnesota, Ontario, Wisconsin↗

USGS2006

A standard protocol for describing individual-based and agent-based models

Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers.

Ecological Modelling↗

USGS2004

Ten suggestions to strengthen the science of ecology

There are few well-documented, general ecological principles that can be applied to pressing environmental issues. When they discuss them at all, ecologists often disagree about the relative importance of different aspects of the science's original and still important issues. It may be that the sum of ecological science is not open to universal statements because of the wide range of organizational, spatial, and temporal phenomena, as well as the sheer number of possible interactions. We believe, however, that the search for general principles has been inadequate to establish the extent to which generalities are possible. We suggest that ecologists may need to reconsider how we view our science. This article lists 10 suggestions for ecology, recognizing the many impediments to finding generalizations in this field, imposed in part by the complexity of the subject and in part by limits to funding for the study of ecology.

Conference Paper↗

USGS2011

Social network models predict movement and connectivity in ecological landscapes

Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

Proceedings of the National Academy of Sciences of↗

USGS2009

A multiscale analysis of coral reef topographic complexity using lidar-derived bathymetry

Coral reefs represent one of the most irregular substrates in the marine environment. This roughness or topographic complexity is an important structural characteristic of reef habitats that affects a number of ecological and environmental attributes, including species diversity and water circulation. Little is known about the range of topographic complexity exhibited within a reef or between different reef systems. The objective of this study was to quantify topographic complexity for a 5-km x 5-km reefscape along the northern Florida Keys reef tract, over spatial scales ranging from meters to hundreds of meters. The underlying dataset was a 1-m spatial resolution, digital elevation model constructed from lidar measurements. Topographic complexity was quantified using a fractal algorithm, which provided a multi-scale characterization of reef roughness. The computed fractal dimensions ( D ) are a measure of substrate irregularity and are bounded between values of 2 and 3. Spatial patterns in D were positively correlated with known reef zonation in the area. Landward regions of the study site contain relatively smooth ( D ≈ 2.35) flat-topped patch reefs, which give way to rougher ( D ≈ 2.5), deep, knoll-shaped patch reefs. The seaward boundary contains a mixture of substrate features, including discontinuous shelf-edge reefs, and exhibits a corresponding range of roughness values (2.28 ≤ D ≤ 2.61).

Journal of Coastal Research↗

USGS2004

Ecoregions and ecoregionalization: geographical and ecological perspectives

Ecoregions, i.e., areas exhibiting relative homogeneity of ecosystems, are units of analysis that are increasingly important in environmental assessment and management. Ecoregions provide a holistic framework for flexible, comparative analysis of complex environmental problems. Ecoregions mapping has intellectual foundations in both geography and ecology. However, a hallmark of ecoregions mapping is that it is a truly interdisciplinary endeavor that demands the integration of knowledge from a multitude of sciences. Geographers emphasize the role of place, scale, and both natural and social elements when delineating and characterizing regions. Ecologists tend to focus on environmental processes with special attention given to energy flows and nutrient cycling. Integration of disparate knowledge from the many key sciences has been one of the great challenges of ecoregions mapping, and may lie at the heart of the lack of consensus on the “optimal” approach and methods to use in such work. Through a review of the principal existing US ecoregion maps, issues that should be addressed in order to advance the state of the art are identified. Research related to needs, methods, data sources, data delivery, and validation is needed. It is also important that the academic system foster education so that there is an infusion of new expertise in ecoregion mapping and use.

Environmental Management↗

USGS2011

Phylogenetic and ecological characteristics associated with thiaminase activity in Laurentian Great Lakes fishes

Thiamine deficiency complex (TDC) causes mortality and sublethal effects in Great Lakes salmonines and results from low concentrations of egg thiamine that are thought to be caused by thiaminolytic enzymes (i.e., thiaminase) present in the diet. This complex has the potential to undermine efforts to restore lake trout Salvelinus namaycush and severely restrict salmonid production in the Great Lakes. Although thiaminase has been found in a variety of Great Lakes fishes, the ultimate source of thiaminase in Great Lakes fishes is currently unknown. We used logistic regression analysis to investigate relationships between thiaminase activity and phylogenetic or ecological characteristics of 39 Great Lakes fish species. The taxonomically more ancestral species were more likely to show thiaminase activity than the more derived species. Species that feed at lower trophic levels and occupy benthic habitats also appeared to be more likely to show thiaminase activity; these variables were correlated with taxonomy, which was the most important predictor of thiaminase activity. Further analyses of the relationship between quantitative measures of thiaminase activity and ecological characteristics of Great Lakes fish species would provide greater insight into potential sources and pathways of thiaminase in Great Lakes food webs. ?? Copyright by the American Fisheries Society 2008.

Transactions of the American Fisheries Society↗

USGS2017

The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

Virus Research↗

USGS2016

Revisiting Paine’s 1966 sea star removal experiment, the most-cited empirical article in the American Naturalist

“Food Web Complexity and Species Diversity” (Paine 1966) is the most-cited empirical article published in the American Naturalist . In short, Paine removed predatory sea stars ( Pisaster ochraceus ) from the rocky intertidal and watched the key prey species, mussels ( Mytilus californianus ), crowd out seven subordinate primary space-holding species. However, because these mussels are a foundational species, they provide three-dimensional habitat for over 300 associated species inhabiting the mussel beds; thus, removing sea stars significantly increases community-wide diversity. In any case, most ecologists cite Paine (1966) to support a statement that predators increase diversity by interfering with competition. Although detractors remained skeptical of top-down effects and keystone concepts, the paradigm that predation increases diversity spread. By 1991, “Food Web Complexity and Species Diversity” was considered a classic ecological paper, and after 50 years it continues to influence ecological theory and conservation biology.

American Naturalist↗

USGS2015

Linking dynamic habitat selection with wading bird foraging distributions across resource gradients

Species distribution models (SDM) link species occurrence with a suite of environmental predictors and provide an estimate of habitat quality when the variable set captures the biological requirements of the species. SDMs are inherently more complex when they include components of a species' ecology such as conspecific attraction and behavioral flexibility to exploit resources that vary across time and space. Wading birds are highly mobile, demonstrate flexible habitat selection, and respond quickly to changes in habitat quality; thus serving as important indicator species for wetland systems. We developed a spatio-temporal, multi-SDM framework using Great Egret ( Ardea alba ), White Ibis ( Eudocimus albus ), and Wood Stork ( Mycteria Americana ) distributions over a decadal gradient of environmental conditions to predict species-specific abundance across space and locations used on the landscape over time. In models of temporal dynamics, species demonstrated conditional preferences for resources based on resource levels linked to differing temporal scales. Wading bird abundance was highest when prey production from optimal periods of inundation was concentrated in shallow depths. Similar responses were observed in models predicting locations used over time, accounting for spatial autocorrelation. Species clustered in response to differing habitat conditions, indicating that social attraction can co-vary with foraging strategy, water-level changes, and habitat quality. This modeling framework can be applied to evaluate the multi-annual resource pulses occurring in real-time, climate change scenarios, or restorative hydrological regimes by tracking changing seasonal and annual distribution and abundance of high quality foraging patches.

PLoS ONE↗

USGS2012

Studying biodiversity: is a new paradigm really needed?

Authors in this journal have recommended a new approach to the conduct of biodiversity science. This data-driven approach requires the organization of large amounts of ecological data, analysis of these data to discover complex patterns, and subsequent development of hypotheses corresponding to detected patterns. This proposed new approach has been contrasted with more-traditional knowledge-based approaches in which investigators deduce consequences of competing hypotheses to be confronted with actual data, providing a basis for discriminating among the hypotheses. We note that one approach is directed at hypothesis generation, whereas the other is also focused on discriminating among competing hypotheses. Here, we argue for the importance of using existing knowledge to the separate issues of (a) hypothesis selection and generation and (b) hypothesis discrimination and testing. In times of limited conservation funding, the relative efficiency of different approaches to learning should be an important consideration in decisions about how to study biodiversity.

BioScience↗

USGS2009

Fort Collins Science Center - Fiscal Year 2008 Science Accomplishments

Open-File Report↗

USGS2010

Fort Collins Science Center-Fiscal year 2009 science accomplishments

Public land and natural resource managers in the United States are confronted with increasingly complex decisions that have important ramifications for both ecological and human systems. The scientists and technical professionals at the U.S. Geological Survey Fort Collins Science Center?many of whom are at the forefront of their fields?possess a unique blend of ecological, socioeconomic, and technological expertise. Because of this diverse talent, Fort Collins Science Center staff are able to apply a systems approach to investigating complicated ecological problems in a way that helps answer critical management questions. In addition, the Fort Collins Science Center has a long record of working closely with the academic community through cooperative agreements and other collaborations. The Fort Collins Science Center is deeply engaged with other U.S. Geological Survey science centers and partners throughout the Department of the Interior. As a regular practice, we incorporate the expertise of these partners in providing a full complement of ?the right people? to effectively tackle the multifaceted research problems of today's resource-management world. In Fiscal Year 2009, the Fort Collins Science Center's scientific and technical professionals continued research vital to Department of the Interior's science and management needs. Fort Collins Science Center work also supported the science needs of other Federal and State agencies as well as non-government organizations. Specifically, Fort Collins Science Center research and technical assistance focused on client and partner needs and goals in the areas of biological information management and delivery, enterprise information, fisheries and aquatic systems, invasive species, status and trends of biological resources (including human dimensions), terrestrial ecosystems, and wildlife resources. In the process, Fort Collins Science Center science addressed natural-science information needs identified in the U.S. Geological Survey Science Strategy (http://www.usgs.gov/science_strategy), including understanding and predicting change in ecosystems, climate variability and change, energy development and land management, the role of the environment and wildlife in human health, freshwater ecosystems, data integration, and evolving technologies. Several science projects were expanded in Fiscal Year 2009 to meet these evolving needs.

Open-File Report↗

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↗

USGS2015

Quantifying the adaptive cycle

The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems.

PLoS ONE↗