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Analysis of neighborhood dynamics of forest ecosystems using likelihood methods and modeling.

Advances in computing power in the past 20 years have led to a proliferation of spatially explicit, individual-based models of population and ecosystem dynamics. In forest ecosystems, the individual-based models encapsulate an emerging theory of "neighborhood" dynamics, in which fine-scale spatial interactions regulate the demography of component tree species. The spatial distribution of component species, in turn, regulates spatial variation in a whole host of community and ecosystem properties, with subsequent feedbacks on component species. The development of these models has been facilitated by development of new methods of analysis of field data, in which critical demographic rates and ecosystem processes are analyzed in terms of the spatial distributions of neighboring trees and physical environmental factors. The analyses are based on likelihood methods and information theory, and they allow a tight linkage between the models and explicit parameterization of the models from field data. Maximum likelihood methods have a long history of use for point and interval estimation in statistics. In contrast, likelihood principles have only more gradually emerged in ecology as the foundation for an alternative to traditional hypothesis testing. The alternative framework stresses the process of identifying and selecting among competing models, or in the simplest case, among competing point estimates of a parameter of a model. There are four general steps involved in a likelihood analysis: (1) model specification, (2) parameter estimation using maximum likelihood methods, (3) model comparison, and (4) model evaluation. Our goal in this paper is to review recent developments in the use of likelihood methods and modeling for the analysis of neighborhood processes in forest ecosystems. We will focus on a single class of processes, seed dispersal and seedling dispersion, because recent papers provide compelling evidence of the potential power of the approach, and illustrate some of the statistical challenges in applying the methods.

Computer Simulation↗

A spatially explicit decision support model for restoration of forest bird habitat.

The historical area of bottomland hardwood forest in the Mississippi Alluvial Valley has been reduced by >75%. Agricultural production was the primary motivator for deforestation; hence, clearing deliberately targeted higher and drier sites. Remaining forests are highly fragmented and hydrologically altered, with larger forest fragments subject to greater inundation, which has negatively affected many forest bird populations. We developed a spatially explicit decision support model, based on a Partners in Flight plan for forest bird conservation, that prioritizes forest restoration to reduce forest fragmentation and increase the area of forest core (interior forest >1 km from "hostile" edge). Our primary objective was to increase the number of forest patches that harbor >2000 ha of forest core, but we also sought to increase the number and area of forest cores >5000 ha. Concurrently, we targeted restoration within local (320 km2) landscapes to achieve > or =60% forest cover Finally, we emphasized restoration of higher-elevation bottomland hardwood forests in areas where restoration would not increase forest fragmentation. Reforestation of 10% of restorable land in the Mississippi Alluvial Valley (approximately 880,000 ha) targeted at priorities established by this decision support model resulted in approximately 824,000 ha of new forest core. This is more than 32 times the amount of core forest added through reforestation of randomly located fields (approximately 25,000 ha). The total area of forest core (1.6 million ha) that resulted from targeted restoration exceeded habitat objectives identified in the Partners in Flight Bird Conservation Plan and approached the area of forest core present in the 1950s.

Animals↗

A spatially explicit model for an Allee effect: why wolves recolonize so slowly in Greater Yellowstone.

A reduced probability of finding mates at low densities is a frequently hypothesized mechanism for a component Allee effect. At low densities dispersers are less likely to find mates and establish new breeding units. However, many mathematical models for an Allee effect do not make a distinction between breeding group establishment and subsequent population growth. Our objective is to derive a spatially explicit mathematical model, where dispersers have a reduced probability of finding mates at low densities, and parameterize the model for wolf recolonization in the Greater Yellowstone Ecosystem (GYE). In this model, only the probability of establishing new breeding units is influenced by the reduced probability of finding mates at low densities. We analytically and numerically solve the model to determine the effect of a decreased probability in finding mates at low densities on population spread rate and density. Our results suggest that a reduced probability of finding mates at low densities may slow recolonization rate.

Acclimatization↗

The spread of infectious diseases in spatially structured populations: an invasory pair approximation.

The invasion of new species and the spread of emergent infectious diseases in spatially structured populations has stimulated the study of explicit spatial models such as cellular automata, network models and lattice models. However, the analytic intractability of these models calls for the development of tractable mathematical approximations that can capture the dynamics of discrete, spatially-structured populations. Here we explore moment closure approximations for the invasion of an SIS epidemic on a regular lattice. We use moment closure methods to derive an expression for the basic reproductive number, R(0), in a lattice population. On lattices, R(0) should be bounded above by the number of neighbors per individual. However, we show that conventional pair approximations actually predict unbounded growth in R(0) with increasing transmission rates. To correct this problem, we propose an 'invasory' pair approximation which yields a relatively simple expression for R(0) that remains bounded above, and also predicts R(0) values from lattice model simulations more accurately than conventional pair and triple approximations. The invasory pair approximation is applicable to any spatial model, since it takes into account characteristics of invasions that are common to all spatially structured populations.

Animals↗

Selection for intermediate mortality and reproduction rates in a spatially structured population.

How local interactions influence both population and evolutionary dynamics is currently a key topic in theoretical ecology. We use a 'well-mixed' analytical model and spatially explicit individual-based models to investigate a system where a population is subject to rare disturbance events. The disturbance can only propagate through regions of the population where the density of individuals is sufficiently high and individuals affected by the disturbance die shortly after. We find that populations where individuals are sessile often exhibit very different dynamic behaviour when compared to populations where individuals are mobile and spatially well mixed. When mutations are allowed which affect either offspring birth rates or mortality rates, the well-mixed populations always evolve to a state where a single disturbance event leads to extinction. Populations often persist substantially longer if individuals are sessile and they disperse their offspring locally. We also find that for sessile populations selection may favour short-lived individuals with limited offspring production. Population dynamics are found to be strongly influenced by the host characters that are evolving and the rate at which host variation is introduced into the system.

Animals↗

Risk based management of contaminated sediments: consideration of spatial and temporal patterns in exposure modeling.

This paper addresses interactions among foraging behavior, habitat preferences, site characteristics, and spatial distribution of contaminants in developing PCB exposure estimates for winter flounder at a hypothetical open water dredged material disposal site in the coastal waters of New York and New Jersey (NY-NJ). The implications of these interactions for human health risk estimates for local recreational anglers who fish for and eat flounder are described. The models implemented in this study include a spatial submodel to account for spatial and temporal characteristics of fish exposures and a probabilistic adaptation of the Gobas bioaccumulation model that accounts for temporal variation in concentrations of hydrophobic contaminants in sediment and water. We estimated the geographic distribution of a winter flounder subpopulation offshore of NY-NJ based on species biology and its vulnerability to local recreational fishing, the foraging area of individual fish, and their migration patterns. We incorporated these parameters and an estimate of differential attraction to a management site into a spatially explicit model to assess the range of exposures within the population. The output of this modeling effort, flounder PCB tissue concentrations, provided exposure point concentrations for an estimate of human health risk through ingestion of locally caught flounder. The risks obtained for the spatially nonexplicit case are as much as 1 order of magnitude higher than those obtained with explicit consideration of spatial and temporal characteristics of winter flounder foraging and seasonal migration. This practice of "defaulting" to extremely conservative estimates for exposure parameters in the face of uncertainty ill serves the decision-making process for management of contaminated sediments in general and specifically for disposal of dredged materials. Consideration of realistic spatial and temporal scales in food chain models can help support sediment management decisions by providing a quantitative expression of the confidence in risk estimates.

Animals↗

A mechanistic model for partial preferences.

Classic prey optimal foraging model assumes that individual predators are globally omniscient; that is, they have exact knowledge of prey population densities in the environment. This study examines a spatially explicit individual-based model of a one-predator two-prey system where individual predators are assumed to be omniscient only locally, i.e., to know prey population densities only in the range of their perception. Due to local variations in prey numbers, the probability of acceptance of less profitable prey shifts from the zero-one rule to a gradually decreasing function, for which an explicit formula is derived, giving way to partial preferences. A corresponding predator functional response to more profitable prey is shown to have a sigmoid-like form.

Animals↗

Patch aging and the S-Allee effect: breeding system effects on the demographic response of plants to habitat fragmentation.

We used empirical and modeling approaches to examine effects of plant breeding systems on demographic responses to habitat fragmentation. Empirically, we investigated effects of local flowering plant density on pollination and of population size on mate availability in a common, self-incompatible purple coneflower, Echinacea angustifolia, growing in fragmented prairie habitat. Pollination and recruitment increased with weighted local density around individual flowering plants. This positive density dependence is an Allee effect. In addition, mean mate compatibility between pairs of plants increased with population size. Based on this empirical study, we developed an individual-based, spatially explicit demographic model that incorporates autosomal loci and an S locus. We simulated habitat fragmentation in populations identical except for their breeding system, self-incompatible (SI) or self-compatible (SC). Both populations suffered reduced reproduction in small patches because of scarcity of plants within pollination distance (potential mates) and inbreeding depression. But SI species experienced an additional, genetic contribution to the Allee effect (S-Allee effect) caused by allele loss at the S locus, which reduces mate availability, thereby decreasing reproduction. The strength of the S-Allee effect increases through time (i.e., patches age) because random genetic drift reduces S-allele richness. We investigate how patch aging influences extinction and discuss how the S-Allee effect influences communities in fragmented habitat.

Breeding↗

Comparing approximations to spatio-temporal models for epidemics with local spread.

Analytical methods for predicting and exploring the dynamics of stochastic, spatially interacting populations have proven to have useful application in epidemiology and ecology. An important development has been the increasing interest in spatially explicit models, which require more advanced analytical techniques than the usual mean-field or mass-action approaches. The general principle is the derivation of differential equations describing the evolution of the expected population size and other statistics. As a result of spatial interactions no closed set of equations is obtained. Nevertheless, approximate solutions are possible using closure relations for truncation. Here we review and report recent progress on closure approximations applicable to lattice models with nearest-neighbour interactions, including cluster approximations and elaborations on the pair (or pairwise) approximation. This study is made in the context of an SIS model for plant-disease epidemics introduced in Filipe and Gibson (1998, Studying and approximating spatio-temporal models for epidemic spread and control, Phil. Trans. R. Soc. Lond. B 353, 2153-2162) of which the contact process [Harris, T. E. (1974), Contact interactions on a lattice, Ann. Prob. 2, 969] is a special case. The various methods of approximation are derived and explained and their predictions are compared and tested against simulation. The merits and limitations of the various approximations are discussed. A hybrid pairwise approximation is shown to provide the best predictions of transient and long-term, stationary behaviour over the whole parameter range of the model.

Cluster Analysis↗

Time and space issues in ecotoxicology: population models, landscape pattern analysis, and long-range environmental chemistry.

Advances in ecotoxicology addressing problems of time and spatial scales are presented and interpreted in the frame of concepts on population/community dynamics and landscape pattern analysis. Example deterministic/probabilistic modeling experiments are used to illustrate key concepts. Space and time scales analyzed are single and multigenerations of local populations, metapopulations, community, and ecosystem/landscape. Most population models used in recent ecotoxicology studies are deterministic and do not include a formal treatment of spatial processes, like migration or local random extinction. Some metapopulation models have been applied with success. Upscaling of ecotoxicological results at the community level is less developed, probably because of the inherent complexity of indirect and direct coactions among organisms. Community and ecosystem toxicity end points that could find a broad use in regulatory applications have not yet been identified. Some practical issues like the estimation of the potential for the natural attenuation of toxicity and the transport of contaminants along food chains must be addressed at these scales/levels of biological complexity. The estimation of ecotoxicological effects has been increasingly evolving to integrate modeling and monitoring contaminant transport and fate, landscape pattern analysis, and spatially explicit population dynamics (including direct and indirect communal interactions).

Agriculture↗

Modelling the impact of climate change on woody plant population dynamics in South African savanna.

BACKGROUND: In Southern Africa savannas climate change has been proposed to alter rainfall, the most important environmental driver for woody plants. Woody plants are a major component of savanna vegetation determining rangeland condition and biodiversity. In this study we use a spatially explicit, stochastic computer model to assess the impact of climate change on the population dynamics of Grewia flava, a common, fleshy-fruited shrub species in the southern Kalahari. Understanding the population dynamics of Grewia flava is a crucial task, because it is widely involved in the shrub/bush encroachment process, a major concern for rangeland management due to its adverse effect on livestock carrying capacity and biodiversity. RESULTS: For our study we consider four climate change scenarios that have been proposed for the southern Kalahari for the coming decades: (1) an increase in annual precipitation by 30-40%, (2) a decrease by 5-15%, (3) an increase in variation of extreme rainfall years by 10-20%, (4) and increase in temporal auto-correlation, i.e. increasing length and variation of periodic rainfall oscillations related to El Nino/La Nina phenomena. We evaluate the slope z of the time-shrub density relationship to quantify the population trend. For each climate change scenario we then compared the departure of z from typical stable population dynamics under current climatic conditions. Based on the simulation experiments we observed a positive population trend for scenario (1) and a negative trend for scenario (2). In terms of the projected rates of precipitation change for scenario (3) and (4) population dynamics were found to be relatively stable. However, for a larger increase in inter-annual variation or in temporal auto-correlation of rainfall population trends were negative, because favorable rainfall years had a limited positive impact due to the limited shrub carrying capacity. CONCLUSIONS: We conclude that a possible increase in precipitation will strongly facilitate shrub encroachment threatening savanna rangeland conditions and regional biodiversity. Furthermore, the negative effects found for positive auto-correlated rainfall support current ecological theory stating that periodically fluctuating environments can reduce population viability because species suffer disproportionately from poor environmental conditions.

Biodiversity↗

Spatiotemporal dynamics in marginal populations.

Population dynamics across a mortality gradient at an ecological margin are investigated using a novel modeling approach that allows direct comparison of stochastic spatially explicit simulation results with deterministic mean field models. The results show that demographic stochasticity has a large effect at population margins such that density profiles fall off more sharply than predicted by mean field models. Substantial spatial structure emerges at the margin, and spatial correlations (measured parallel to the margin) exhibit a sharp maximum in the tail of the density profile, indicating that spatial substructuring is greatest at an intermediate point across the ecological gradient. Such substructuring may have a substantial impact on Allee effects and evolutionary processes in marginal populations.

Animals↗

The use of spatial modeling in an aquatic food web to estimate exposure and risk.

This paper quantitatively evaluates interactions among foraging behavior, habitat preferences, site characteristics and the spatial distribution of contaminants in estimating PCB exposure concentrations for winter flounder at a hypothetical open water dredged material disposal site in the coastal waters of New York and New Jersey (NY-NJ). The models implemented in this study include a spatial submodel to account for spatial and temporal characteristics of fish exposure and a probabilistic adaptation of the Gobas bioaccumulation model to account for temporal variation in concentrations of polychlorinated biphenyls (PCBs) in sediment and water. We estimated the geographic distribution of an offshore winter flounder subpopulation based on species biology, including such variables as foraging area, habitat size, disposal site size and migration characteristics. We incorporated these variables together with an estimate of differential attraction to a management site within a spatially explicit model to assess the range of expected PCB exposures to a winter flounder population. The output of this modeling effort, flounder PCB tissue concentrations, provides exposure point concentrations for estimates of human health risk through ingestion of locally caught flounder. The risks obtained for the spatially non-explicit case are as much as one order of magnitude higher than those obtained after incorporating spatial and temporal characteristics of winter flounder foraging and seasonal migration. Incorporating spatial and temporal variables in food chain models can help support sediment management decisions by providing a quantitative expression of the confidence in risk estimates.

Animals↗

Coupled map lattice approximations for spatially explicit individual-based models of ecology.

Spatially explicit individual-based models are widely used in ecology but they are often difficult to treat analytically. Despite their intractability they often exhibit clear temporal and spatial patterning. We demonstrate how a spatially explicit individual-based model of scramble competition with local dispersal can be approximated by a stochastic coupled map lattice. The approximation disentangles the deterministic and stochastic element of local interaction and dispersal. We are thus able to understand the individual-based model through a simplified set of equations. In particular, we demonstrate that demographic noise leads to increased stability in the dynamics of locally dispersing single-species populations. The coupled map lattice approximation has general application to a range of spatially explicit individual-based models. It provides a new alternative to current approximation techniques, such as the method of moments and reaction-diffusion approximation, that captures both stochastic effects and large-scale patterning arising in individual-based models.

Animals↗

A dispersal model for the range expansion of blacklegged tick (Acari: Ixodidae).

The blacklegged tick, Ixodes scapularis Say, a vector for the agents of Lyme borreliosis and other diseases, has expanded its range dramatically over the past 20 yr. However, the relative contributions of different vertebrate host species to this expansion have remained largely unexplored. To address this issue, we simulated the expansion of a theoretical tick population across a simple landscape by using a deterministic, spatially explicit, cellular automata model. The model incorporates the ecology of ticks and three vertebrate hosts: white-tailed deer, Odocoileus virginianus Zimmermann; white-footed mouse, Peromyscus leucopus Rafinesque; and American robin, Turdus migratorius L. Host contribution to tick dispersal is modeled as a function of tick burden, home range size, and population density. These parameters were determined using published and unpublished data. Our results suggest that 1) hosts with high tick burdens and large home ranges (e.g., deer) play a critical role in I. scapularis range expansion; 2) hosts with small home ranges (e.g., mice) can limit range expansion if they divert a sufficient number of ticks from feeding on more mobile hosts; and (3) birds that migrate annually (e.g., robins) can play a crucial role in tick range expansion.

Animals↗

Sustainable trophy hunting of African lions.

In most species, sport hunting of male trophy animals can only reduce overall population size when the rate of removal of males is so high that females can no longer be impregnated. However, where males provide extensive paternal care, the removal of even a few individuals could harm the population as a whole. In species such as lions, excessive trophy hunting could theoretically cause male replacements (and associated infanticide) to become sufficiently common to prevent cubs reaching adulthood. Here we simulate the population consequences of lion trophy hunting using a spatially explicit, individual-based, stochastic model parameterized with 40 years of demographic data from northern Tanzania. Although our simulations confirm that infanticide increases the risk of population extinction, trophy hunting could be sustained simply by hunting males above a minimum age threshold, and this strategy maximizes both the quantity and the quality of the long-term kill. We present a simple non-invasive technique for estimating lion age in populations lacking long-term records, and suggest that quotas would be unnecessary in any male-only trophy species where age determination could be reliably implemented.

Age Factors↗

Habitat fragmentation resulting in overgrazing by herbivores.

Habitat fragmentation sometimes results in outbreaks of herbivorous insect and causes an enormous loss of primary production. It is hypothesized that the driving force behind such herbivore outbreaks is disruption of natural enemy attack that releases herbivores from top-down control. To test this hypothesis I studied how trophic community structure changes along a gradient of habitat fragmentation level using spatially implicit and explicit models of a tri-trophic (plant, herbivore and natural enemy) food chain. While in spatially implicit model number of trophic levels gradually decreases with increasing fragmentation, in spatially explicit model a relatively low level of habitat fragmentation leads to overgrazing by herbivore to result in extinction of the plant population followed by a total system collapse. This provides a theoretical support to the hypothesis that habitat fragmentation can lead to overgrazing by herbivores and suggests a central role of spatial structure in the influence of habitat fragmentation on trophic communities. Further, the spatially explicit model shows (i) that the total system collapse by the overgrazing can occur only if herbivore colonization rate is high; (ii) that with increasing natural enemy colonization rate, the fragmentation level that leads to the system collapse becomes higher, and the frequency of the collapse is lowered.

Animals↗

Dynamics and management of infectious disease in colonizing populations.

The introduction of chronic, infectious diseases by colonizing populations (invasive or reintroduced) is a serious hazard in conservation biology, threatening the original host and other spillover species. Most research on spatial invasion of diseases has pertained to established host populations, either at steady state or fluctuating through time. Within a colonizing population, however, the spread of disease may be influenced by the expansion process of the population itself. Here we explore the simultaneous expansion of a colonizing population and a chronic, nonlethal disease introduced with it, describing basic patterns in homogeneous and structured landscapes and discussing implications for disease management. We describe expected outcomes of such introductions for three qualitatively distinct cases, depending on the relative velocities at which the population and epidemic expand. (1) If transmissibility is low the disease cannot be sustained, although it may first expand its range somewhat around the point of introduction. (2) If transmissibility is moderate but the wave-front velocity for the population, vp, is higher than that for the disease, vd, the disease wave front lags behind that of the population. (3) A highly transmissible disease, with vd > vp, will invade sufficiently rapidly to track the spread of the host. To test these elementary theoretical predictions, we simulated disease outbreaks in a spatially structured host population occupying a real landscape. We used a spatially explicit, individual-based model of Persian fallow deer (Dama mesopotamica) reintroduced in northern Israel, considering a hypothetical introduction of bovine tuberculosis. Basic patterns of disease expansion in this realistic setting were similar to our conceptual predictions for homogeneous landscapes. Landscape heterogeneity, however, induced the establishment of population activity centers and disease foci within them, leading to jagged wave fronts and causing local variation in the relative velocities at which the population and epidemic expanded. Based on predictions from simple theory and simulations of managed outbreaks, we suggest that the relative velocities at which the population and epidemic expand have important implications for the impact of different management strategies. Recognizing which of our three general cases best describes a particular outbreak will aid in planning an efficient strategy to contain the disease.

Animals↗