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At least 793 records · Page 44Linked to original sources

Model weights and the foundations of multimodel inference

Statistical thinking in wildlife biology and ecology has been profoundly influenced by the introduction of AIC (Akaike?s information criterion) as a tool for model selection and as a basis for model averaging. In this paper, we advocate the Bayesian paradigm as a broader framework for multimodel inference, one in which model averaging and model selection are naturally linked, and in which the performance of AIC-based tools is naturally evaluated. Prior model weights implicitly associated with the use of AIC are seen to highly favor complex models: in some cases, all but the most highly parameterized models in the model set are virtually ignored a priori. We suggest the usefulness of the weighted BIC (Bayesian information criterion) as a computationally simple alternative to AIC, based on explicit selection of prior model probabilities rather than acceptance of default priors associated with AIC. We note, however, that both procedures are only approximate to the use of exact Bayes factors. We discuss and illustrate technical difficulties associated with Bayes factors, and suggest approaches to avoiding these difficulties in the context of model selection for a logistic regression. Our example highlights the predisposition of AIC weighting to favor complex models and suggests a need for caution in using the BIC for computing approximate posterior model weights.

Ecology↗

GIS-based rapid-assessment of bighead carp Hypophthalmichthys nobilis (Richardson, 1845) suitability in reservoirs

Broad-scale niche models are good for examining the potential for invasive species occurrences, but can fall short in providing managers with site-specific locations for monitoring. Using Oklahoma as an example, where invasive bighead carp (Hypophthalmichthys nobilis) are established in certain reservoirs, but predicted to be widely distributed based on broad-scale niche models, we cast bighead carp reproductive ecology in a site-specific geospatial framework to determine their potential establishment in additional reservoirs. Because bighead carp require large, long free-flowing rivers with suitable hydrology for reproduction but can persist in reservoirs, we considered reservoir tributaries with mean annual daily discharge ≥8.5 cubic meters per second (m3 /s) and quantified the length of their unimpeded portions. In contrast to published broad-scale niche models that identified nearly the entire state as susceptible to invasion, our site-specific models showed that few reservoirs in Oklahoma (N = 9) were suitable for bighead carp establishment. Moreover, this method was rapid and identified sites that could be prioritized for increased study or scrutiny. Our results highlight the importance of considering the environmental characteristics of individual sites, which is often the level at which management efforts are implemented when assessing susceptibility to invasion.

Oklahoma↗

Consequences of gas flux model choice on the interpretation of metabolic balance across 15 lakes

Ecosystem metabolism and the contribution of carbon dioxide from lakes to the atmosphere can be estimated from free-water gas measurements through the use of mass balance models, which rely on a gas transfer coefficient ( k ) to model gas exchange with the atmosphere. Theoretical and empirically based models of k range in complexity from wind-driven power functions to complex surface renewal models; however, model choice is rarely considered in most studies of lake metabolism. This study used high-frequency data from 15 lakes provided by the Global Lake Ecological Observatory Network (GLEON) to study how model choice of k influenced estimates of lake metabolism and gas exchange with the atmosphere. We tested 6 models of k on lakes chosen to span broad gradients in surface area and trophic states; a metabolism model was then fit to all 6 outputs of k data. We found that hourly values for k were substantially different between models and, at an annual scale, resulted in significantly different estimates of lake metabolism and gas exchange with the atmosphere.

Inland Waters↗

Taking a systems approach to ecological systems

Increasingly, there is interest in a systems-level understanding of ecological problems, which requires the evaluation of more complex, causal hypotheses. In this issue of the Journal of Vegetation Science, Soliveres et al. use structural equation modeling to test a causal network hypothesis about how tree canopies affect understorey communities. Historical analysis suggests structural equation modeling has been under-utilized in ecology.

Journal of Vegetation Science↗

Narrowing historical uncertainty: probabilistic classification of ambiguously identified tree species in historical forest survey data

Historical data have increasingly become appreciated for insight into the past conditions of ecosystems. Uses of such data include assessing the extent of ecosystem change; deriving ecological baselines for management, restoration, and modeling; and assessing the importance of past conditions on the composition and function of current systems. One historical data set of this type is the Public Land Survey (PLS) of the United States General Land Office, which contains data on multiple tree species, sizes, and distances recorded at each survey point, located at half-mile (0.8 km) intervals on a 1-mi (1.6 km) grid. This survey method was begun in the 1790s on US federal lands extending westward from Ohio. Thus, the data have the potential of providing a view of much of the US landscape from the mid-1800s, and they have been used extensively for this purpose. However, historical data sources, such as those describing the species composition of forests, can often be limited in the detail recorded and the reliability of the data, since the information was often not originally recorded for ecological purposes. Forest trees are sometimes recorded ambiguously, using generic or obscure common names. For the PLS data of northern Wisconsin, USA, we developed a method to classify ambiguously identified tree species using logistic regression analysis, using data on trees that were clearly identified to species and a set of independent predictor variables to build the models. The models were first created on partial data sets for each species and then tested for fit against the remaining data. Validations were conducted using repeated, random subsets of the data. Model prediction accuracy ranged from 81% to 96% in differentiating congeneric species among oak, pine, ash, maple, birch, and elm. Major predictor variables were tree size, associated species, landscape classes indicative of soil type, and spatial location within the study region. Results help to clarify ambiguities formerly present in maps of historic ecosystems for the region and can be applied to PLS datasets elsewhere, as well as other sources of ambiguous historical data. Mapping the newly classified data with ecological land units provides additional information on the distribution, abundance, and associations of tree species, as well as their relationships to environmental gradients before the industrial period, and clarifies the identities of species formerly mapped only to genus. We offer some caveats on the appropriate use of data derived in this way, as well as describing their potential.

Ecosystems↗

Landscape genetic approaches to guide native plant restoration in the Mojave Desert

Restoring dryland ecosystems is a global challenge due to synergistic drivers of disturbance coupled with unpredictable environmental conditions. Dryland plant species have evolved complex life-history strategies to cope with fluctuating resources and climatic extremes. Although rarely quantified, local adaptation is likely widespread among these species and potentially influences restoration outcomes. The common practice of reintroducing propagules to restore dryland ecosystems, often across large spatial scales, compels evaluation of adaptive divergence within these species. Such evaluations are critical to understanding the consequences of large-scale manipulation of gene flow and to predicting success of restoration efforts. However, genetic information for species of interest can be difficult and expensive to obtain through traditional common garden experiments. Recent advances in landscape genetics offer marker-based approaches for identifying environmental drivers of adaptive genetic variability in non-model species, but tools are still needed to link these approaches with practical aspects of ecological restoration. Here, we combine spatially-explicit landscape genetics models with flexible visualization tools to demonstrate how cost-effective evaluations of adaptive genetic divergence can facilitate implementation of different seed sourcing strategies in ecological restoration. We apply these methods to Amplified Fragment Length Polymorphism (AFLP) markers genotyped in two Mojave Desert shrub species of high restoration importance: the long-lived, wind-pollinated gymnosperm Ephedra nevadensis , and the short-lived, insect-pollinated angiosperm Sphaeralcea ambigua . Mean annual temperature was identified as an important driver of adaptive genetic divergence for both species. Ephedra showed stronger adaptive divergence with respect to precipitation variability, while temperature variability and precipitation averages explained a larger fraction of adaptive divergence in Sphaeralcea . We describe multivariate statistical approaches for interpolating spatial patterns of adaptive divergence while accounting for potential bias due to neutral genetic structure. Through a spatial bootstrapping procedure, we also visualize patterns in the magnitude of model uncertainty. Finally, we introduce an interactive, distance-based mapping approach that explicitly links marker-based models of adaptive divergence with local or admixture seed sourcing strategies, promoting effective native plant restoration.

Mojave Desert↗

Use of multiple temperature logger models can alter conclusions

Remote temperature loggers are often used to measure water temperatures for ecological studies and by regulatory agencies to determine whether water quality standards are being maintained. Equipment specifications are often given a cursory review in the methods; however, the effect of temperature logger model is rarely addressed in the discussion. In a laboratory environment, we compared measurements from three models of temperature loggers at 5 to 40 °C to better understand the utility of these devices. Mean water temperatures recorded by logger models differed statistically even for those with similar accuracy specifications, but were still within manufacturer accuracy specifications. Maximum mean temperature difference between models was 0.4 °C which could have regulatory and ecological implications, such as when a 0.3 °C temperature change triggers a water quality violation or increases species mortality rates. Additionally, precision should be reported as the overall precision (including a consideration of significant digits) for combined model types which in our experiment was 0.7 °C, not the ≤0.4 °C for individual models. Our results affirm that analyzing data collected by different logger models can result in potentially erroneous conclusions when <1 °C difference has regulatory compliance or ecological implications and that combining data from multiple logger models can reduce the overall precision of results.

Water↗

Circuit theory and model-based inference for landscape connectivity

Circuit theory has seen extensive recent use in the field of ecology, where it is often applied to study functional connectivity. The landscape is typically represented by a network of nodes and resistors, with the resistance between nodes a function of landscape characteristics. The effective distance between two locations on a landscape is represented by the resistance distance between the nodes in the network. Circuit theory has been applied to many other scientific fields for exploratory analyses, but parametric models for circuits are not common in the scientific literature. To model circuits explicitly, we demonstrate a link between Gaussian Markov random fields and contemporary circuit theory using a covariance structure that induces the necessary resistance distance. This provides a parametric model for second-order observations from such a system. In the landscape ecology setting, the proposed model provides a simple framework where inference can be obtained for effects that landscape features have on functional connectivity. We illustrate the approach through a landscape genetics study linking gene flow in alpine chamois (Rupicapra rupicapra) to the underlying landscape.

Journal of the American Statistical Association↗

Sensitivity of system stability to model structure

A community is stable, and resilient, if the levels of all community variables can return to the original steady state following a perturbation. The stability properties of a community depend on its structure, which is the network of direct effects (interactions) among the variables within the community. These direct effects form feedback cycles (loops) that determine community stability. Although feedback cycles have an intuitive interpretation, identifying how they form the feedback properties of a particular community can be intractable. Furthermore, determining the role that any specific direct effect plays in the stability of a system is even more daunting. Such information, however, would identify important direct effects for targeted experimental and management manipulation even in complex communities for which quantitative information is lacking. We therefore provide a method that determines the sensitivity of community stability to model structure, and identifies the relative role of particular direct effects, indirect effects, and feedback cycles in determining stability. Structural sensitivities summarize the degree to which each direct effect contributes to stabilizing feedback or destabilizing feedback or both. Structural sensitivities prove useful in identifying ecologically important feedback cycles within the community structure and for detecting direct effects that have strong, or weak, influences on community stability. The approach may guide the development of management intervention and research design. We demonstrate its value with two theoretical models and two empirical examples of different levels of complexity. ?? 2009 Elsevier B.V. All rights reserved.

Ecological Modelling↗

Exploring metapopulation-scale suppression alternatives for a global invader in a river network experiencing climate change

Invasive species can dramatically alter ecosystems, but eradication is difficult, and suppression is expensive once they are established. Uncertainties in the potential for expansion and impacts by an invader can lead to delayed and inadequate suppression, allowing for establishment. Metapopulation viability models can aid in planning strategies to improve responses to invaders and lessen invasive species’ impacts, which may be particularly important under climate change. We used a spatially explicit metapopulation viability model to explore suppression strategies for ecologically damaging invasive brown trout ( Salmo trutta ), established in the Colorado River and a tributary in Grand Canyon National Park. Our goals were to estimate the effectiveness of strategies targeting different life stages and subpopulations within a metapopulation; quantify the effectiveness of a rapid response to a new invasion relative to delaying action until establishment; and estimate whether future hydrology and temperature regimes related to climate change and reservoir management affect metapopulation viability and alter the optimal management response. Our models included scenarios targeting different life stages with spatially varying intensities of electrofishing, redd destruction, incentivized angler harvest, piscicides, and a weir. Quasi-extinction (QE) was obtainable only with metapopulation-wide suppression targeting multiple life stages. Brown trout population growth rates were most sensitive to changes in age 0 and large adult mortality. The duration of suppression needed to reach QE for a large established subpopulation was 12 years compared with 4 with a rapid response to a new invasion. Isolated subpopulations were vulnerable to suppression; however, connected tributary subpopulations enhanced metapopulation persistence by serving as climate refuges. Water shortages driving changes in reservoir storage and subsequent warming would cause brown trout declines, but metapopulation QE was achieved only through refocusing and increasing suppression. Our modeling approach improves understanding of invasive brown trout metapopulation dynamics, which could lead to more focused and effective invasive species suppression strategies and, ultimately, maintenance of populations of endemic fishes.

Arizona↗

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&ndash;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↗

Hierarchical models of animal abundance and occurrence

Much of animal ecology is devoted to studies of abundance and occurrence of species, based on surveys of spatially referenced sample units. These surveys frequently yield sparse counts that are contaminated by imperfect detection, making direct inference about abundance or occurrence based on observational data infeasible. This article describes a flexible hierarchical modeling framework for estimation and inference about animal abundance and occurrence from survey data that are subject to imperfect detection. Within this framework, we specify models of abundance and detectability of animals at the level of the local populations defined by the sample units. Information at the level of the local population is aggregated by specifying models that describe variation in abundance and detection among sites. We describe likelihood-based and Bayesian methods for estimation and inference under the resulting hierarchical model. We provide two examples of the application of hierarchical models to animal survey data, the first based on removal counts of stream fish and the second based on avian quadrat counts. For both examples, we provide a Bayesian analysis of the models using the software WinBUGS.

Journal of Agricultural, Biological, and Environme↗

How well do proxy species models inform conservation of surrogate species?

Context Proxy species, which represent suites of organisms with similar habitat requirements, are common in conservation. Landscape Capability (LC) models aim to quantify the spatially-explicit capability of landscapes to support proxy species that represent suites of forest birds. Objectives We evaluated the North Atlantic Landscape Conservation Cooperative (NALCC) proxy models of LC and represented species framework across 13 states in the northeastern United States from Virginia to Maine. We validated a suite of questions related to co-occurrence of proxy and represented species with a compilation of independent datasets. Methods We tested proxy species LC models ability to explain represented species’ occurrences, including using multiple proxies together, and benchmarked against empirical data and land cover type classifications. We tested effect of several factors on predictive ability including relative range overlap and ecological and taxonomic dissimilarity between proxy and represented species. Results LC models performed variably, but represented species occurrences were rarely predicted as accurately as proxy species. Models improved predictions over macrohabitat classifications. Using multiple proxies together occasionally improved predictions of represented species. Considerable range overlap was needed for models to be predictive of represented species. Ecological and taxonomic similarity had no effect on predictive ability. LC models worked similarly to using empirical observations, suggesting shortcomings were because of imperfect surrogacy. Conclusions Conservation proxies as representatives of species groups that are associated with macrohabitats are useful, but empirical data are necessary to evaluate proxy species’ effectiveness. Habitat-based models can provide similar predictive ability as empirical observations of proxies and represent a useful tool in conservation planning.

Landscape Ecology↗

Putting flow-ecology relationships into practice: A decision-support system to assess fish community response to water-management scenarios

This paper presents a conceptual framework to operationalize flow–ecology relationships into decision-support systems of practical use to water-resource managers, who are commonly tasked with balancing multiple competing socioeconomic and environmental priorities. We illustrate this framework with a case study, whereby fish community responses to various water-management scenarios were predicted in a partially regulated river system at a local watershed scale. This case study simulates management scenarios based on interactive effects of dam operation protocols, withdrawals for municipal water supply, effluent discharges from wastewater treatment, and inter-basin water transfers. Modeled streamflow was integrated with flow–ecology relationships relating hydrologic departure from reference conditions to fish species richness, stratified by trophic, reproductive, and habitat characteristics. Adding a hypothetical new water-withdrawal site was predicted to increase the frequency of low-flow conditions with adverse effects for several fish groups. Imposition of new reservoir release requirements was predicted to enhance flow and fish species richness immediately downstream of the reservoir, but these effects were dissipated further downstream. The framework presented here can be used to translate flow–ecology relationships into evidence-based management by developing decision-support systems for conservation of riverine biodiversity while optimizing water availability for human use.

Water↗

Integrating behavior and physiology into strategies for amphibian conservation

The amphibian decline crisis has been challenging to address because of the complexity of factors—and their multitude of interactive effects—that drive this global issue. Dissecting such complexity could benefit from strategies that integrate multiple disciplines and address the mechanistic underpinnings of population declines and extirpations. We examine how the disciplines of behavior and physiology could be used to develop conservation strategies for amphibians and identify eight research gaps that provide future directions for the emerging fields of conservation behavior and conservation physiology. We present two case studies on imperiled salamanders that show how studies of behavior and physiology may support amphibian conservation efforts. We found several applications of stress physiology to amphibian conservation, but long-term studies are needed to understand how stress ultimately affects individual fitness and population resilience. Additionally, multiple measures of physiological health are needed to provide a more holistic assessment of an individual’s overall condition. Previous behavioral and physiological studies have been instrumental for understanding how amphibians respond to habitat modification, pathogens and parasites, contaminants, and invasive species. Some behavior-based approaches to mitigating invasive species issues have been successful in short-term studies with individual species. However, widespread application of these tactics has not yet been integrated into conservation and management strategies for ecologically-similar species. A diversity of modeling approaches has enhanced understanding of how climate change may impact amphibian populations, but model predictions need empirical tests to provide conservation managers with workable approaches to multiple perturbations associated with global environmental change. We illustrate that behavior and physiology can have broad utility for amphibian conservation, but evidence is scant that such studies have actually been used to inform strategies for amphibian conservation and management.

Frontiers in Ecology and Evolution↗

Enhanced understanding of ectoparasite: host trophic linkages on coral reefs through stable isotope analysis

Parasitism, although the most common type of ecological interaction, is usually ignored in food web models and studies of trophic connectivity. Stable isotope analysis is widely used in assessing the flow of energy in ecological communities and thus is a potentially valuable tool in understanding the cryptic trophic relationships mediated by parasites. In an effort to assess the utility of stable isotope analysis in understanding the role of parasites in complex coral-reef trophic systems, we performed stable isotope analysis on three common Caribbean reef fish hosts and two kinds of ectoparasitic isopods: temporarily parasitic gnathiids ( Gnathia marleyi ) and permanently parasitic cymothoids ( Anilocra ) . To further track the transfer of fish-derived carbon (energy) from parasites to parasite consumers, gnathiids from host fish were also fed to captive Pederson shrimp ( Ancylomenes pedersoni ) for at least 1 month. Parasitic isopods had &delta; 13 C and &delta; 15 N values similar to their host, comparable with results from the small number of other host&ndash;parasite studies that have employed stable isotopes. Adult gnathiids were enriched in 15 N and depleted in 13 C relative to juvenile gnathiids, providing insights into the potential isotopic fractionation associated with blood-meal assimilation and subsequent metamorphosis. Gnathiid-fed Pedersen shrimp also had &delta; 13 C values consistent with their food source and enriched in 15 N as predicted due to trophic fractionation. These results further indicate that stable isotopes can be an effective tool in deciphering cryptic feeding relationships involving parasites and their consumers, and the role of parasites and cleaners in carbon transfer in coral-reef ecosystems specifically.

Lameshur Bay, St. John, Virgin Islands↗

Potential for real‐time understanding of coupled hydrologic and biogeochemical processes in stream ecosystems: Future integration of telemetered data with process models for glacial meltwater streams

While continuous monitoring of streamflow and temperature has been common for some time, there is great potential to expand continuous monitoring to include water quality parameters such as nutrients, turbidity, oxygen, and dissolved organic material. In many systems, distinguishing between watershed and stream ecosystem controls can be challenging. The usefulness of such monitoring can be enhanced by the application of quantitative models to interpret observed patterns in real time. Examples are discussed primarily from the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. Although the Dry Valley landscape is barren of plants, many streams harbor thriving cyanobacterial mats. Whereas a daily cycle of streamflow is controlled by the surface energy balance on the glaciers and the temporal pattern of solar exposure, the daily signal for biogeochemical processes controlling water quality is generated along the stream. These features result in an excellent outdoor laboratory for investigating fundamental ecosystem process and the development and validation of process‐based models. As part of the McMurdo Dry Valleys Long‐Term Ecological Research project, we have conducted field experiments and developed coupled biogeochemical transport models for the role of hyporheic exchange in controlling weathering reactions, microbial nitrogen cycling, and stream temperature regulation. We have adapted modeling approaches from sediment transport to understand mobilization of stream biomass with increasing flows. These models help to elucidate the role of in‐stream processes in systems where watershed processes also contribute to observed patterns, and may serve as a test case for applying real‐time stream ecosystem models.

Water Resources Research↗

Experts correctly describe demography associated with historical decline of the endangered Indiana bat, but not recent period of stationarity

Demographic characteristics of bats are often insufficiently described for modeling populations. In data poor situations, experts are often relied upon for characterizing ecological systems. In concert with the development of a matrix model describing Indiana bat ( Myotis sodalis ) demography, we elicited estimates for parameterizing this model from 12 experts. We conducted this elicitation in two stages, requesting expert values for 12 demographic rates. These rates were adult and juvenile seasonal (winter, summer, fall) survival rates, pup survival in fall, and propensity and success at breeding. Experts were most in agreement about adult fall survival (3% Coefficient of Variation) and least in agreement about propensity of juveniles to breed (37% CV). The experts showed greater concordance for adult ( mean CV, adult = 6.2%) than for juvenile parameters ( mean CV, juvenile = 16.4%), and slightly more agreement for survival (mean CV, survival = 9.8%) compared to reproductive rates ( mean CV, reproduction = 15.1%). However, survival and reproduction were negatively and positively biased, respectively, relative to a stationary dynamic. Despite the species exhibiting near stationary dynamics for two decades prior to the onset of a potential extinction-causing agent, white-nose syndrome, expert estimates indicated a population decline of -11% per year (95% CI = -2%, -20%); quasi-extinction was predicted within a century ( mean = 61 years to QE, range = 32, 97) by 10 of the 12 experts. Were we to use these expert estimates in our modeling efforts, we would have errantly trained our models to a rapidly declining demography asymptomatic of recent demographic behavior. While experts are sometimes the only source of information, a clear understanding of the temporal and spatial context of the information being elicited is necessary to guard against wayward predictions.

PeerJ↗