Tropical deforestation in Madagascar: analysis using hierarchical,spatially explicit,Bayesian regression models

Establishing cause–effect relationships for deforestation at various scales has proven difficult even when rates of deforestation appear well documented. There is a need for better explanatory models, which also provide insight into the process of deforestation. We propose a novel hierarchical modeling specification incorporating spatial association. The hierarchical aspect allows us to accommodate misalignment between the land-use (response) data layer and explanatory data layers. Spatial structure seems appropriate due to the inherently spatial nature of land use and data layers explaining land use. Typically, there will be missing values or holes in the response data. To accommodate this we propose an imputation strategy. We apply our modeling approach to develop a novel deforestation model for the eastern wet forested zone of Madagascar, a global rain forest “hot spot”. Using five data layers created for this region, we fit a suitable spatial hierarchical model. Though fitting such models is computationally much more demanding than fitting more standard models, we show that the resulting interpretation is much richer. Also, we employ a model choice criterion to argue that our fully Bayesian model performs better than simpler ones. To the best of our knowledge, this is the first work that applies hierarchical Bayesian modeling techniques to study deforestation processes. We conclude with a discussion of our findings and an indication of the broader ecological applicability of our modeling style.     

Design and validation of a spatially explicit simulation model for bottomland hardwood forests

Species composition in forests depends on the interaction of species traits and species availability. Yet many forest simulation models focus only on interactions of adult trees and saplings, ignoring how species become members of the community. We modify a published forest model for bottomland hardwood forests (program SWAMP [Phipps, R.L., 1979. Simulation of wetlands forest vegetation dynamics. Ecol. Modell. 7, 257–288]) to make it spatially explicit and incorporate explicit seed production and dispersal algorithms. The resulting individual-based, spatially explicit forest simulator (YAFSIM) combines mechanistic seed dispersal with growth and mortality of trees to track forest dynamics over time. We describe the structure of the model and test its validity for dynamics in small bottomland hardwood patches in the Mississippi Alluvial Valley. Dynamics of species composition and basal areas of trees predicted by Yazoo Forest Simulator (YAFSIM) were similar to those of natural second- and old-growth bottomland forests. However, diversity of simulated forest patches declined over time largely because of random dynamics acting on small, isolated populations.     

Insights from life history theory for an explicit treatment of trade‐offs in conservation biology

As economic and social contexts become more embedded within biodiversity conservation, it becomes obvious that resources are a limiting factor in conservation. This recognition is leading conservation scientists and practitioners to increasingly frame conservation decisions as trade‐offs between conflicting societal objectives. However, this framing is all too often done in an intuitive way, rather than by addressing trade‐offs explicitly. In contrast, the concept of trade‐off is a keystone in evolutionary biology, where it has been investigated extensively. I argue that insights from evolutionary theory can provide methodological and theoretical support to evaluating and quantifying trade‐offs in biodiversity conservation. I reviewed the diverse ways in which trade‐offs have emerged within the context of conservation and how advances from evolutionary theory can help avoid the main pitfalls of an implicit approach. When studying both evolutionary trade‐offs (e.g., reproduction vs. survival) and conservation trade‐offs (e.g., biodiversity conservation vs. agriculture), it is crucial to correctly identify the limiting resource, hold constant the amount of this resource when comparing different scenarios, and choose appropriate metrics to quantify the extent to which the objectives have been achieved. Insights from studies in evolutionary theory also reveal how an inadequate selection of conservation solutions may result from considering suboptimal rather than optional solutions when examining whether a trade‐off exits between 2 objectives. Furthermore, the shape of a trade‐off curve (i.e., whether the relationship between 2 objectives follows a concave, convex, or linear form) is known to affect crucially the definition of optimal solutions in evolutionary biology and very likely affects decisions in biodiversity conservation planning too. This interface between evolutionary biology and biodiversity conservation can therefore provide methodological guidance to support decision makers in the difficult task of choosing among conservation solutions. Percepciones de la Teoría de Historia de Vida para una Tratamiento Explícito de las Compensaciones en la Biología de la Conservación     

Determining the drivers of population structure in a highly urbanized landscape to inform conservation planning

Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human‐dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home‐range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11–81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions.     

The need for spatially explicit quantification of benefits in invasive‐species management

Worldwide, invasive species are a leading driver of environmental change across terrestrial, marine, and freshwater environments and cost billions of dollars annually in ecological damages and economic losses. Resources limit invasive‐species control, and planning processes are needed to identify cost‐effective solutions. Thus, studies are increasingly considering spatially variable natural and socioeconomic assets (e.g., species persistence, recreational fishing) when planning the allocation of actions for invasive‐species management. There is a need to improve understanding of how such assets are considered in invasive‐species management. We reviewed over 1600 studies focused on management of invasive species, including flora and fauna. Eighty‐four of these studies were included in our final analysis because they focused on the prioritization of actions for invasive species management. Forty‐five percent (n = 38) of these studies were based on spatial optimization methods, and 35% (n = 13) accounted for spatially variable assets. Across all 84 optimization studies considered, 27% (n = 23) explicitly accounted for spatially variable assets. Based on our findings, we further explored the potential costs and benefits to invasive species management when spatially variable assets are explicitly considered or not. To include spatially variable assets in decision‐making processes that guide invasive‐species management there is a need to quantify environmental responses to invasive species and to enhance understanding of potential impacts of invasive species on different natural or socioeconomic assets. We suggest these gaps could be filled by systematic reviews, quantifying invasive species impacts on native species at different periods, and broadening sources and enhancing sharing of knowledge.     

Robust population management under uncertainty for structured population models.

Structured population models are increasingly used in decision making, but typically have many entries that are unknown or highly uncertain. We present an approach for the systematic analysis of the effect of uncertainties on long-term population growth or decay. Many decisions for threatened and endangered species are made with poor or no information. We can still make decisions under these circumstances in a manner that is highly defensible, even without making assumptions about the distribution of uncertainty, or limiting ourselves to discussions of single, infinitesimally small changes in the parameters. Suppose that the model (determined by the data) for the population in question predicts long-term growth. Our goal is to determine how uncertain the data can be before the model loses this property. Some uncertainties will maintain long-term growth, and some will lead to long-term decay. The uncertainties are typically structured, and can be described by several parameters. We show how to determine which parameters maintain long-term growth. We illustrate the advantages of the method by applying it to a Peregrine Falcon population. The U.S. Fish and Wildlife Service recently decided to allow minimal harvesting of Peregrine Falcons after their recent removal from the Endangered Species List. Based on published demographic rates, we find that an asymptotic growth rate lambda > 1 is guaranteed with 5% harvest rate up to 3% error in adult survival if no two-year-olds breed, and up to 11% error if all two-year-olds breed. If a population growth rate of 3% or greater is desired, the acceptable error in adult survival decreases to between 1% and 6% depending of the proportion of two-year-olds that breed. These results clearly show the interactions between uncertainties in different parameters, and suggest that a harvest decision at this stage may be premature without solid data on adult survival and the frequency of breeding by young adults.     

Comparison of statistical and theoretical habitat models for conservation planning: the benefit of ensemble prediction

Selection of a modeling approach is an important step in the conservation planning process, but little guidance is available. We compared two statistical and three theoretical habitat modeling approaches representing those currently being used for avian conservation planning at landscape and regional scales: hierarchical spatial count (HSC), classification and regression tree (CRT), habitat suitability index (HSI), forest structure database (FS), and habitat association database (HA). We focused our comparison on models for five priority forest-breeding species in the Central Hardwoods Bird Conservation Region: Acadian Flycatcher, Cerulean Warbler, Prairie Warbler, Red-headed Woodpecker, and Worm-eating Warbler. Lacking complete knowledge on the distribution and abundance of each species with which we could illuminate differences between approaches and provide strong grounds for recommending one approach over another, we used two approaches to compare models: rank correlations among model outputs and comparison of spatial correspondence. In general, rank correlations were significantly positive among models for each species, indicating general agreement among the models. Worm-eating Warblers had the highest pairwise correlations, all of which were significant (P < 0.05). Red-headed Woodpeckers had the lowest agreement among models, suggesting greater uncertainty in the relative conservation value of areas within the region. We assessed model uncertainty by mapping the spatial congruence in priorities (i.e., top ranks) resulting from each model for each species and calculating the coefficient of variation across model ranks for each location. This allowed identification of areas more likely to be good targets of conservation effort for a species, those areas that were least likely, and those in between where uncertainty is higher and thus conservation action incorporates more risk. Based on our results, models developed independently for the same purpose (conservation planning for a particular species in a particular geography) yield different answers and thus different conservation strategies. We assert that using only one habitat model (even if validated) as the foundation of a conservation plan is risky. Using multiple models (i.e., ensemble prediction) can reduce uncertainty and increase efficacy of conservation action when models corroborate one another and increase understanding of the system when they do not.     

Hidden process models for animal population dynamics.

Hidden process models are a conceptually useful and practical way to simultaneously account for process variation in animal population dynamics and measurement errors in observations and estimates made on the population. Process variation, which can be both demographic and environmental, is modeled by linking a series of stochastic and deterministic subprocesses that characterize processes such as birth, survival, maturation, and movement. Observations of the population can be modeled as functions of true abundance with realistic probability distributions to describe observation or estimation error. Computer-intensive procedures, such as sequential Monte Carlo methods or Markov chain Monte Carlo, condition on the observed data to yield estimates of both the underlying true population abundances and the unknown population dynamics parameters. Formulation and fitting of a hidden process model are demonstrated for Sacramento River winter-run chinook salmon (Oncorhynchus tshawytsha).     

Incorporating private lands in conservation planning: protected areas in Britain.

Evaluations of the effectiveness of protected areas often report their inadequate representation of regional variation in environmental conditions, land cover, and biological diversity. One frequent contributory explanation is the heavy reliance placed upon the designation of public as opposed to private lands for statutory protection. Given that protected area designation in Britain has no such constraint, and indeed that more than half of such areas are on private lands, we tested the a priori assumption that within this region the representation of environmental conditions and land cover within statutory protected areas would be more equitable. Despite the reduction in land ownership constraints on where protected areas can be established, a marked bias in protected area coverage remains. Protected areas in Britain tend toward regions of higher elevation, soils of lower economic potential, and coastal/estuarine habitat and fail adequately to represent areas of lower elevation and woodland habitats. Improving the current situation requires not only a more systematic approach to site selection, but a more equitable and diverse portfolio of incentives for private landowners to facilitate the decision to manage sites for conservation.     

COSMOS,a spatially explicit model to simulate the epidemiology of Cosmopolites sordidus in banana fields

A stochastic individual-based model called COSMOS was developed to simulate the epidemiology of banana weevil Cosmopolites sordidus, a major pest of banana fields. The model is based on simple rules of local movement of adults, egg laying of females, development and mortality, and infestation of larvae inside the banana plants. The biological parameters were estimated from the literature, and the model was validated at the small-plot scale. Simulated and observed distributions of attacks were similar except for five plots out of 18, using a Kolmogorov–Smirnov test. These exceptions may be explained by variation in predation of eggs and measurement error. An exhaustive sensitivity analysis using the Morris method showed that predation rate of eggs, demographic parameters of adults and mortality rate of larvae were the most influential parameters. COSMOS was therefore used to test different spatial arrangements of banana plants on the epidemiology of C. sordidus. Planting bananas in groups increased the time required to colonise plots but also the percentage of banana plants with severe attacks. Spatial heterogeneity of banana stages had no effect on time required to colonise plots but increased the mean level of attacks. Our model helps explain key factors of population dynamics and the epidemiology of this tropical pest.     

Integration of a fish bioenergetics model into a spatially explicit water quality model: Application to menhaden in Chesapeake Bay

Although fish are usually thought of as victims of water quality degradation, it has been proposed that some planktivorous species may improve water quality through consumption of algae and sequestering of nutrients via growth. Within most numerical water quality models, the highest trophic level modeled explicitly is zooplankton, prohibiting an investigation of the effect a fish species may be having on its environment. Conversely, numerical models of fish consumption do not typically include feedback mechanisms to capture the effects of fish on primary production and nutrient recycling. In the present study, a fish bioenergetics model is incorporated into CE-QUAL-ICM, a spatially explicit eutrophication model. In addition to fish consumption of algae, zooplankton, and detritus, fish biomass accumulation and nutrient recycling to the water column are explicitly accounted for. These developments advance prior modeling efforts of the impact of fish on water quality, many of which are based on integrated estimates over an entire system and which omit the feedback the fish have through nutrient recycling and excretion. To validate the developments, a pilot application was undertaken for Atlantic menhaden (Brevoortia tyrannus) in Chesapeake Bay. The model indicates menhaden may reduce the algal biomass while simultaneously increasing primary productivity.     

A mixed methodology for evaluating use of evidence in conservation planning

Conservation practitioners widely recognize the importance of making decisions based on the best available evidence. However, the effectiveness of evidence use in conservation planning is rarely assessed, which limits opportunities to improve evidence-based practice. We devised a mixed methodology for empirically evaluating use of evidence that applies social science tools to systematically appraise what kinds of evidence are used in conservation planning, to what effect, and under what limitations. We applied our approach in a case study of the Nature Conservancy of Canada (NCC), a leading land conservation organization. We conducted qualitative and quantitative analyses of 65 NCC planning documents (n = 13 in-depth) to identify patterns in evidence use, and surveyed 35 conservation planners to examine experiences of and barriers to using evidence. Although claims in plans contained a wide range of evidence types, 26% of claims were not referenced or associated with an identifiable source. Lack of evidence use was particularly apparent in claims associated with direct threats, particularly those identified as low (71% coded as insufficient or lacking evidence) or medium (45%) threats. Survey participants described relying heavily on practitioner experience and highlighted capacity limitations and disciplinary gaps in expertise among planning teams as barriers to using evidence effectively. We found that although time-intensive, this approach yielded actionable recommendations for improving evidence use in NCC conservation plans. Similar mixed-method assessments may streamline the process by including interviews and refining the document analysis frames to target issues or sections of concern. We suggest our method provides an accessible and robust point of departure for conservation practitioners to evaluate whether the use of conservation planning reflects in-house standards and more broadly recognized best practices.     

Practitioner insights as a means of setting a context for conservation

A key obstacle to conservation success is the tendency of conservation professionals to tackle each challenge individually rather than collectively and in context. We sought to prioritize barriers to conservation previously described in the conservation literature. We undertook an online survey of 154 practitioners from over 70 countries to ascertain the most important barriers to conservation they faced. We used statistical analyses to identify the key impediments to conservation success and to examine whether these were affected by organizational attributes. Twenty-one barriers were identified. The importance ascribed to those was influenced by continent of operation and organization size, but not by organization age or autonomy (from larger parent organizations). We found the most important barriers to consider when undertaking conservation action were wider issues (e.g., population growth, consumerism, favoring development, and industrial-scale activity), operating environment (e.g., lack of political will, ineffective law enforcement, weak governments, corruption, safety and security), community attributes (e.g., dynamics, conflicts, and education levels), and the way conservation is undertaken (overconfidence, lack of funding, and externally set agendas). However, we advise against applying a one-size-fits-all approach. We propose that conservationists account for the complex socioecological systems they operate in if they are to achieve success.     

Chlorophyll fluorescence as a proxy for microphytobenthic biomass: alternatives to the current methodology

Pulse amplitude modulated (PAM) fluorescence has been used as a proxy of microphytobenthic biomass after a dark adaptation period of 15 min to stabilise the minimum fluorescence yield (F _o ¹⁵). This methodology was investigated for in situ migratory and ex situ engineered non-migratory biofilms, comparing dark adaptation to low (5% ambient) and far-red light treatments over different emersion periods. Far-red and low light reduced potential errors resulting from light history effects, by reversal of non-photochemical quenching after 5 min of treatment, compared to over 10 min required by conventional dark adaptation. An in situ decline of minimum fluorescence yield over 15 min was observed during the dark adaptation for migratory biofilms, but was not observed in the non-migratory biofilms indicating that the major cause of decline was downward vertical migration of cells into the sediment. This pattern occurred in far-red light after 10 min, but not for the low light treatment, indicating that low light maintained the biomass at the surface of the sediment. It is therefore concluded that low light treatment is a better option than conventional dark adaptation for the measurement of minimum fluorescence as a proxy of microphytobenthic biomass.     

Adaptive introgression as a resource for management and genetic conservation in a changing climate

Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species’ and populations’ ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species’ ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced‐generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.     

Emotion as a source of moral understanding in conservation

Recent debates around the meaning and implications of compassionate conservation suggest that some conservationists consider emotion a false and misleading basis for moral judgment and decision making. We trace these beliefs to a long-standing, gendered sociocultural convention and argue that the disparagement of emotion as a source of moral understanding is both empirically and morally problematic. According to the current scientific and philosophical understanding, reason and emotion are better understood as partners, rather than opposites. Nonetheless, the two have historically been seen as separate, with reason elevated in association with masculinity and emotion (especially nurturing emotion) dismissed or delegitimated in association with femininity. These associations can be situated in a broader, dualistic, and hierarchical logic used to maintain power for a dominant male (White, able-bodied, upper class, heterosexual) human class. We argue that emotion should be affirmed by conservationists for the novel and essential insights it contributes to conservation ethics. We consider the specific example of compassion and characterize it as an emotional experience of interdependence and shared vulnerability. This experience highlights conservationists’ responsibilities to individual beings, enhancing established and widely accepted beliefs that conservationists have a duty to protect populations, species, and ecosystems (or biodiversity). We argue compassion, thus understood, should be embraced as a core virtue of conservation.     

A comparison of three empirically based, spatially explicit predictive models of residential soil Pb concentrations in Baltimore, Maryland, USA: understanding the variability within cities

In many older US cities, lead (Pb) contamination of residential soil is widespread; however, contamination is not uniform. Empirically based, spatially explicit models can assist city agencies in addressing this important public health concern by identifying areas predicted to exceed public health targets for soil Pb contamination. Sampling of 61 residential properties in Baltimore City using field portable X-ray fluorescence revealed that 53 % had soil Pb that exceeded the USEPA reportable limit of 400 ppm. These data were used as the input to three different spatially explicit models: a traditional general linear model (GLM), and two machine learning techniques: classification and regression trees (CART) and Random Forests (RF). The GLM revealed that housing age, distance to road, distance to building, and the interactions between variables explained 38 % of the variation in the data. The CART model confirmed the importance of these variables, with housing age, distance to building, and distance to major road networks determining the terminal nodes of the CART model. Using the same three predictor variables, the RF model explained 42 % of the variation in the data. The overall accuracy, which is a measure of agreement between the model and an independent dataset, was 90 % for the GLM, 83 % for the CART model, and 72 % for the RF model. A range of spatially explicit models that can be adapted to changing soil Pb guidelines allows managers to select the most appropriate model based on public health targets.     

Governance baselines as a basis for adaptive marine spatial planning

A marine spatial planning (MSP) initiative—if to be successful—has to be rooted in a thorough understanding of the tradition and structures of the governance system in the area targeted for the initiative. After decades of a mainly sectoral approach towards maritime affairs, governments began to recognised the need for a governance framework that applies a more integrated approach to maritime policy. The new Integrated Maritime Policy of the European Union is only one example for such a changed way of policy and decision making. The assembly of a governance baseline can help to identify the crucial hindering and success factors for the implementation of MSP. A governance baseline has two parts. Part One focuses upon the past and current performance of the governance system as it has responded—or failed to respond—to changes in the condition of ecosystems in a specific locale. Part Two of a baseline outlines a strategic approach to the design of a new program and records the goals, objectives and strategies of MSP implementation. Focus on both governance processes and their outcomes is essential and forms the core justification for documenting governance responses to ecosystem change.     

Translocation of threatened plants as a conservation measure in China

We assessed the current status of plant conservation translocation efforts in China, a topic poorly reported in recent scientific literature. We identified 222 conservation translocation cases involving 154 species, of these 87 were Chinese endemic species and 101 (78%) were listed as threatened on the Chinese Species Red List. We categorized the life form of each species and, when possible, determined for each case the translocation type, propagule source, propagule type, and survival and reproductive parameters. A surprisingly large proportion (26%) of the conservation translocations in China were conservation introductions, largely implemented in response to large‐scale habitat destruction caused by the Three‐Gorge Dam and another hydropower project. Documentation and management of the translocations varied greatly. Less than half the cases had plant survival records. Statistical analyses showed that survival percentages were significantly correlated with plant life form and the type of planting materials. Thirty percent of the cases had records on whether or not individuals flowered or fruited. Results of information theoretic model selection indicated that plant life form, translocation type, propagule type, propagule source, and time since planting significantly influenced the likelihood of flowering and fruiting on the project level. We suggest that the scientific‐based application of species conservation translocations should be promoted as part of a commitment to species recovery management. In addition, we recommend that the common practice of within and out of range introductions in nature reserves to be regulated more carefully due to its potential ecological risks. We recommend the establishment of a national office and database to coordinate conservation translocations in China. Our review effort is timely considering the need for a comprehensive national guideline for the newly announced nation‐wide conservation program on species with extremely small populations, which is expected to stimulate conservation translocations for many species in the near future.