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Results for “spatially explicit population models”

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PubMed2006

Genetic structure is influenced by landscape features: empirical evidence from a roe deer population.

The delimitation of population units is of primary importance in population management and conservation biology. Moreover, when coupled with landscape data, the description of population genetic structure can provide valuable knowledge about the permeability of landscape features, which is often difficult to assess by direct methods (e.g. telemetry). In this study, we investigated the genetic structuring of a roe deer population which recently recolonized a fragmented landscape. We sampled 1148 individuals from a 40 x 55-km area containing several putative barriers to deer movements, and hence to gene flow, namely a highway, rivers and several canals. In order to assess the effect of these landscape features on genetic structure, we implemented a spatial statistical model known as geneland which analyses genetic structure, explicitly taking into account the spatial nature of the problem. Two genetic units were inferred, exhibiting a very low level of differentiation (F(ST) = 0.008). The location of their boundaries suggested that there are no absolute barriers in this study area, but that the combination of several landscape features with low permeability can lead to population differentiation. Our analysis hence suggests that the landscape has a significant influence on the structuring of the population under study. It also illustrates the use of geneland as a powerful method to infer population structure, even in situations of young populations exhibiting low genetic differentiation.

Animals↗

PubMed2005

An agent-based and spatially explicit model of pathogen dissemination in the intensive care unit.

OBJECTIVE: To develop and disseminate a spatially explicit model of contact transmission of pathogens in the intensive care unit. DESIGN: A model simulating the spread of a pathogen transmitted by direct contact (such as methicillin-resistant Staphylococcus aureus or vancomycin-resistant Enterococcus) was constructed. The modulation of pathogen dissemination attending changes in clinically relevant pathogen- and institution-specific factors was then systematically examined. SETTING AND PATIENTS: The model was configured as a hypothetical 24-bed intensive care unit. The model can be parameterized with different pathogen transmissibilities, durations of caregiver and/or patient contamination, and caregiver allocation and flow patterns. INTERVENTIONS: Pathogen- and institution-specific factors examined included pathogen transmissibility, duration of caregiver contamination, regional cohorting of contaminated or infected patients, delayed detection and isolation of newly contaminated patients, reduction of the number of caregiver visits, and alteration of caregiver allocation among patients. MEASUREMENTS AND MAIN RESULTS: The model predicts the probability that a given fraction of the population will become contaminated or infected with the pathogen of interest under specified spatial, initial prevalence, and dynamic conditions. Per-encounter pathogen acquisition risk and the duration of caregiver pathogen carriage most strongly affect dissemination. Regional cohorting and rapid detection and isolation of contaminated patients each markedly diminish the likelihood of dissemination even absent other interventions. Strategies reducing "crossover" between caregiver domains diminish the likelihood of more widespread dissemination. CONCLUSIONS: Spatially explicit discrete element models, such as the model presented, may prove useful for analyzing the transmission of pathogens within the intensive care unit.

Caregivers↗

PubMed2006

A spatially explicit approach to estimating species occupancy and spatial correlation.

1. Understanding and predicting the form of species distributions, or occupancy patterns, is fundamental to macroecology and is dependent on the identification of scaling relationships that underlie the patterns observed. 2. Occupancy-abundance models based on the negative binomial distribution and Taylor's power law are spatially implicit, rather than explicit, as they include no information on the relative positions of individuals. Here we present a spatially explicit model, the spatial scaling occupancy (SSO) model, to estimate species occupancy and spatial correlation, based on join-count statistics, or a pair approximation, approach. This model provides a spatially explicit description of species range size and aspects of range structure. 3. Occupancy data from Drosophilidae species inhabiting a decaying fruit mesocosm were used to test the SSO model. Predictions from the spatially implicit and explicit models were largely equally accurate. The SSO model is thus more efficient as it is less data demanding, and more informative as it provides an estimation of spatial correlation. 4. The results also showed that species distribution patterns differ when examined with spatially implicit vs. explicit approaches; the scaling relationship between occupancy and local density identifies a focal grain for studying the scale-dependent nature of ecological relationships; and the longer the length of the sample edge, the higher the occupancy observed under conditions of spatial aggregation. 5. The SSO model presents a step towards a general scaling model for occupancy, and demonstrates that the inclusion of spatially explicit information in macroecological models warrants further attention.

Animals↗

PubMed2000

The potential of geographical information systems and remote sensing in the epidemiology and control of human helminth infections.

Geographic information systems (GIS) and remote sensing (RS) technologies are being used increasingly to study the spatial and temporal patterns of infectious diseases. For helminth infections, however, such applications have only recently begun despite the recognition that infection distribution patterns in endemic areas may have profound effects on parasite population dynamics and therefore the design and implementation of successful control programmes. Here, we review the early applications of these technologies to the major human helminths (geohelminths, schistosomes and the major lymphatic filarial worms), which demonstrate the potential of these tools to serve as: (1) an effective data capture, mapping and analysis tool for the development of helminth atlases; (2) an environment for modeling the spatial distribution of infection in relation to RS and environmental variables, hence furthering the understanding of the impact of density-independent factors in underlying observed parasite spatial distributions and their effective prediction; and (3) a focal tool in parasite control programming given their abilities to (i) better define endemic areas, (ii) provide more precise estimates of populations-at-risk, (iii) map their distribution in relation to health facilities and (iv) by facilitating the stratification of areas by infection risk probabilities, to aid in the design of optimal drug or health measure delivery systems. These applications suggest a successful role for GIS/RS applications in investigating the spatial epidemiology of the major human helminths. It is evident that further work addressing a range of critical issues include problems of data quality, the need for a better understanding of the population biological impact of environmental factors on critical stages of the parasite life-cycle, the impacts and consequences of spatial scale on these relationships, and the development and use of appropriate spatially-explicit statistical and modeling techniques in data analysis, is required if the true potential of this tool to helminthology is to be fully realized.

Animals↗

PubMed2006

Abundance, spatial variance and occupancy: arthropod species distribution in the Azores.

1. The positive abundance-occupancy and abundance-variance relationships are two of the most widely documented patterns in population and community ecology. 2. Recently, a general model has been proposed linking the mean abundance, the spatial variance in abundance, and the occupancy of species. A striking feature of this model is that it consists explicitly of the three variables abundance, variance and occupancy, and no extra parameters are involved. However, little is known about how well the model performs. 3. Here, we show that the abundance-variance-occupancy model fits extremely well to data on the abundance, variance and occupancy of a large number of arthropod species in natural forest patches in the Azores, at three spatial extents, and distinguishing between species of different colonization status. Indeed, virtually all variation about the bivariate abundance-occupancy and abundance-variance relationships is effectively explained by the third missing variable (variance in abundance in the case of the abundance-occupancy relationship, and occupancy in the case of the abundance-variance relationship). 4. Introduced species tend to exhibit lower densities, less spatial variance in these densities, and occupy fewer sites than native and endemic species. None the less, they all lie on the same bivariate abundance-occupancy and abundance-variance, and trivariate abundance-variance-occupancy, relationships. 5. Density, spatial variance in density, and occupancy appear to be all the things one needs to know to describe much of the spatial distribution of species.

Animals↗

PubMed2001

A case study comparing static and spatially explicit ecological exposure analysis methods.

Exposure to chemical contaminants must be estimated when performing ecological risk assessments. A previous article proposed a habitat area and quality conditioned population exposure estimator, E[HQ]P, and described an individual-based, random walk, Monte Carlo model (SE3M) to facilitate calculation of E[HQ]P. In this article, E[HQ]P was compared with exposure estimates from a baseline risk assessment that evaluated mink and great blue heron exposure to fluoride at a federal Superfund site. Calculation of E[HQ]P took into consideration a receptor's forage area, movement behavior, population size, and the areal extent and quality of suitable habitat. The baseline assessment used four methods that did (total and unit Tier 2) and did not (total and unit Tier 1) consider habitat area or quality; where "total" included all exposure units on site and "unit" only a given exposure unit. Total Tier 1 estimates were consistently higher than E[HQ]P (e.g., 169.1 mg/kg x d versus 21.6 mg/kg x d). Risk managers using total Tier 1 results for decision making would be unlikely to underestimate exposure; however, implementability of correspondingly lower remedial objectives could be challenging. Unit Tier 1 estimates were higher (e.g., 96.5 mg/kg x d versus 61.6 mg/kg x d) or lower (e.g., 3.5 mg/kg x d versus 51.1 mg/kg x d) than E[HQ]P depending on variations in landscape features. Total Tier 2 and E[HQ]P estimates were similar (e.g., 20.7 mg/kg x d versus 21.6 mg/kg x d) when an ecologically questionable average exposure was assumed. Unit Tier 2 estimates were consistently well below E[HQ]P (e.g., 17.8 mg/kg x d versus 61.6 mg/kg x d) when an average exposure was not assumed. Risk managers using unit Tier 1 or 2 results could be basing their decisions on potentially large underestimates of exposure. By forgoing average exposure assumptions, and explicitly addressing landscape heterogeneity, SE3M appears capable of yielding exposure estimates that are not as potentially misleading to risk managers as those produced with traditional averaging methods.

Aluminum↗

PubMed2005

Metapopulations in multifractal landscapes: on the role of spatial aggregation.

The use of fractals in ecology is currently pervasive over many areas. However, very few studies have linked fractal properties of landscapes to generating ecological mechanisms and dynamics. In this study I show that lacunarity (a measure of the landscape texture) is a well suited ecologically scaled landscape index that can be explicitly incorporated in metapopulation models such as the classical Levins equation. I show that the average lacunarity of an aggregated landscape is linearly correlated to the habitat that a species with local spatial processed information may perceive. Lacunarity is a computationally feasible index to measure, and is related to the metapopulation capacity of landscapes. A general approach to multifractal landscapes has been conceived, and some analytical results for self-similar landscapes are outlined, including the specific effect of landscape heterogeneity, decoupled from that of contagion by dispersal. Spatially explicit simulations show agreement with the semi-implicit method presented.

Demography↗

PubMed2000

Modeling and analysis of stochastic invasion processes.

In this paper we derive spatially explicit equations to describe a stochastic invasion process. Parents are assumed to produce a random number of offspring which then disperse according to a spatial redistribution kernel. Equations for population moments, such as expected density and covariance averaged over an ensemble of identical stochastic processes, take the form of deterministic integro-difference equations. These equations describe the spatial spread of population moments as the invasion progresses. We use the second order moments to analyse two basic properties of the invasion. The first property is 'permanence of form' in the correlation structure of the wave. Analysis of the asymptotic form of the invasion wave shows that either (i) the covariance in the leading edge of the wave of invasion asymptotically achieves a permanence of form with a characteristic structure described by an unchanging spatial correlation function, or (ii) the leading edge of the wave has no asymptotic permanence of form with the length scales of spatial correlations continually increasing over time. Which of these two outcomes pertains is governed by a single statistic, phi which depends upon the shape of the dispersal kernel and the net reproductive number. The second property of the invasion is its patchy structure. Patchiness, defined in terms of spatial correlations on separate short (within patch) and long (between patch) spatial scales, is linked to the dispersal kernel. Analysis shows how a leptokurtic dispersal kernel gives rise to patchiness in spread of a population.

Animals↗

PubMed2005

The geographic spread of the CCR5 Delta32 HIV-resistance allele.

The Delta32 mutation at the CCR5 locus is a well-studied example of natural selection acting in humans. The mutation is found principally in Europe and western Asia, with higher frequencies generally in the north. Homozygous carriers of the Delta32 mutation are resistant to HIV-1 infection because the mutation prevents functional expression of the CCR5 chemokine receptor normally used by HIV-1 to enter CD4+ T cells. HIV has emerged only recently, but population genetic data strongly suggest Delta32 has been under intense selection for much of its evolutionary history. To understand how selection and dispersal have interacted during the history of the Delta32 allele, we implemented a spatially explicit model of the spread of Delta32. The model includes the effects of sampling, which we show can give rise to local peaks in observed allele frequencies. In addition, we show that with modest gradients in selection intensity, the origin of the Delta32 allele may be relatively far from the current areas of highest allele frequency. The geographic distribution of the Delta32 allele is consistent with previous reports of a strong selective advantage (>10%) for Delta32 carriers and of dispersal over relatively long distances (>100 km/generation). When selection is assumed to be uniform across Europe and western Asia, we find support for a northern European origin and long-range dispersal consistent with the Viking-mediated dispersal of Delta32 proposed by G. Lucotte and G. Mercier. However, when we allow for gradients in selection intensity, we estimate the origin to be outside of northern Europe and selection intensities to be strongest in the northwest. Our results describe the evolutionary history of the Delta32 allele and establish a general methodology for studying the geographic distribution of selected alleles.

Alleles↗

PubMed2005

Disease threats posed by alien species: the role of a poxvirus in the decline of the native red squirrel in Britain.

Red squirrels are declining in the United Kingdom. Competition from, and squirrel poxvirus (SQPV) disease carried by, grey squirrels are assumed to be determining the decline. We analyse the incidence of disease and changes in distribution of the two species in Cumbria, from 1993 to 2003 and compare these to the predictions of an individual-based (IB) spatially explicit disease model simulating the dynamics of both squirrel species and SQPV in the landscape. Grey squirrels increased whilst red squirrels declined over 10 years. The incidence of disease in red squirrels was related to the time since grey squirrels arrived in the landscape. Analysis of rates of decline in red squirrel populations in other areas showed that declines are 17-25 times higher in regions where SQPV is present in grey squirrel populations than in those where it is not. The IB model predicted spatial overlap of 3-4 years between the species that was also observed in the field. The model predictions matched the observed data best when contact rates and rates of infection between the two species were low. The model predicted that a grey squirrel population control of >60% effective kill was needed to stop the decline in red squirrel populations in Cumbria.

Animals↗

PubMed2026

Pattern Formation in a Spatial Public Goods Dilemma due to Diffusive or Directed Motion.

The costly provision of public goods serves as a model problem for the evolution of cooperative behavior, presenting a social dilemma between the collective benefits of shared resources and the individual incentive to free-ride in resource production. The spatial structure of populations can also impact cooperation over public goods, as diffusion of public goods and intentional motion of individuals towards regions with greater resources can interact with population and public goods dynamics to produce heterogeneous patterns in the spatial distribution of strategies and resources. In this paper, we build off a model introduced by Young and Belmonte for the reaction dynamics of interacting individuals and an explicit public good, deriving a system of PDEs that describes the spatial profiles of strategies and the public good in the presence of both diffusive motion of individuals and resources and chemotaxis-like directed motion of individuals in response to gradients in the concentration of public goods. Through linear stability analysis, we show that spatial patterns in strategic and public goods profiles can emerge due to either Turing instability with high defector diffusivity or a directed-motion instability through strong sensitivity of cooperators towards increasing resource concentration. We further explore the emergent spatial patterns with a mix of weakly nonlinear stability analysis and numerical simulation, showing that, for a wide range of reaction parameters, diffusion-driven instability appears to increase cooperation and public goods across the spatial domain, while directed motion of cooperators towards public goods tends to decrease cooperation and environmental quality across the environment.

Models, Biological↗

PubMed2006

Effects of heterogeneity on spread and persistence in rivers.

The question how aquatic populations persist in rivers when individuals are constantly lost due to downstream drift has been termed the "drift paradox." Recent modeling approaches have revealed diffusion-mediated persistence as a solution. We study logistically growing populations with and without a benthic stage and consider spatially varying growth rates. We use idealized hydrodynamic equations to link river cross-sectional area to flow speed and assume heterogeneity in the form of alternating patches, i.e., piecewise constant conditions. We derive implicit formulae for the persistence boundary and for the dispersion relation of the wave speed. We explicitly discuss the influence of flow speed, cross-sectional area and benthic stage on both persistence and upstream invasion speed.

Animals↗

PubMed2002

Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875).

Comparative phylogeography has proved useful for investigating biological responses to past climate change and is strongest when combined with extrinsic hypotheses derived from the fossil record or geology. However, the rarity of species with sufficient, spatially explicit fossil evidence restricts the application of this method. Here, we develop an alternative approach in which spatial models of predicted species distributions under serial paleoclimates are compared with a molecular phylogeography, in this case for a snail endemic to the rainforests of North Queensland, Australia. We also compare the phylogeography of the snail to those from several endemic vertebrates and use consilience across all of these approaches to enhance biogeographical inference for this rainforest fauna. The snail mtDNA phylogeography is consistent with predictions from paleoclimate modeling in relation to the location and size of climatic refugia through the late Pleistocene-Holocene and broad patterns of extinction and recolonization. There is general agreement between quantitative estimates of population expansion from sequence data (using likelihood and coalescent methods) vs. distributional modeling. The snail phylogeography represents a composite of both common and idiosyncratic patterns seen among vertebrates, reflecting the geographically finer scale of persistence and subdivision in the snail. In general, this multifaceted approach, combining spatially explicit paleoclimatological models and comparative phylogeography, provides a powerful approach to locating historical refugia and understanding species' responses to them.

Animals↗

PubMed2001

Brucellosis, botflies, and brainworms: the impact of edge habitats on pathogen transmission and species extinction.

Ecological interactions between species that prefer different habitat types but come into contact in edge regions at the interfaces between habitat types are modeled via reaction-diffusion systems. The primary sort of interaction described by the models is competition mediated by pathogen transmission. The models are somewhat novel because the spatial domains for the variables describing the population densities of the interacting species overlap but do not coincide. Conditions implying coexistence of the two species or the extinction of one species are derived. The conditions involve the principal eigenvalues of elliptic operators arising from linearizations of the model system around equilibria with only one species present. The conditions for persistence or extinction are made explicit in terms of the parameters of the system and the geometry of the underlying spatial domains via estimates of the principal eigenvalues. The implications of the models with respect to conservation and refuge design are discussed.

Animals↗

PubMed1999

Local frequency dependence and global coexistence.

In sessile organisms such as plants, interactions occur locally so that important ecological aspects like frequency dependence are manifest within local neighborhoods. Using probabilistic cellular automata models, we investigated how local frequency-dependent competition influenced whether two species could coexist. Individuals of the two species were randomly placed on a grid and allowed to interact according to local frequency-dependent rules. For four different frequency-dependent scenarios, the results indicated that over a broad parameter range the two species could coexist. Comparisons between explicit spatial simulations and the mean-field approximation indicate that coexistence occurs over a broader region in the explicit spatial simulation.

Ecosystem↗

PubMed2001

Sex-biased gene flow in spectacled eiders (Anatidae): inferences from molecular markers with contrasting modes of inheritance.

Genetic markers that differ in mode of inheritance and rate of evolution (a sex-linked Z-specific microsatellite locus, five biparentally inherited microsatellite loci, and maternally inherited mitochondrial [mtDNA] sequences) were used to evaluate the degree of spatial genetic structuring at macro- and microgeographic scales, among breeding regions and local nesting populations within each region, respectively, for a migratory sea duck species, the spectacled eider (Somateria fisheri). Disjunct and declining breeding populations coupled with sex-specific differences in seasonal migratory patterns and life history provide a series of hypotheses regarding rates and directionality of gene flow among breeding populations from the Indigirka River Delta, Russia, and the North Slope and Yukon-Kuskokwim Delta, Alaska. The degree of differentiation in mtDNA haplotype frequency among breeding regions and populations within regions was high (phiCT = 0.189, P < 0.01; phiSC = 0.059, P < 0.01, respectively). Eleven of 17 mtDNA haplotypes were restricted to a single breeding region. Genetic differences among regions were considerably lower for nuclear DNA loci (sex-linked: phiST = 0.001, P > 0.05; biparentally inherited microsatellites: mean theta = 0.001, P > 0.05) than was observed for mtDNA. Using models explicitly designed for uniparental and biparentally inherited genes, estimates of spatial divergence based on nuclear and mtDNA data together with elements of the species' breeding ecology were used to estimate effective population size and degree of male and female gene flow. Differences in the magnitude and spatial patterns of gene correlations for maternally inherited and nuclear genes revealed that females exhibit greater natal philopatry than do males. Estimates of generational female and male rates of gene flow among breeding regions differed markedly (3.67 x 10(-4) and 1.28 x 10(-2), respectively). Effective population size for mtDNA was estimated to be at least three times lower than that for biparental genes (30,671 and 101,528, respectively). Large disparities in population sizes among breeding areas greatly reduces the proportion of total genetic variance captured by dispersal, which may accelerate rates of inbreeding (i.e., promote higher coancestries) within populations due to nonrandom pairing of males with females from the same breeding population.

Animals↗

PubMed2002

Sexual and vegetative reproduction of Hieracium pilosella L. under competition and disturbance: a grid-based simulation model.

We used a spatially explicit simulation model to examine the relative importance of vegetative and sexual reproduction in Hieracium pilosella L. Based on an understanding of the complex life cycle of this species and on data from in situ population dynamics in a calcareous grassland in NW Switzerland, we simulated growth and the relative contribution of clonal reproduction by stolons and reproduction by seeds across a gradient of increasing soil fertility. Competition by a clonal grass resulted in nearly complete exclusion of H. pilosella from the more fertile part of the simulation plot. Under low soil fertility, when grass could not survive, H. pilosella largely persisted by vegetatively produced rosettes. This pattern of a sharp separation of both species was shifted slightly in favour of H. pilosella by introducing random disturbances. Only by adding: (1) long-distance seed dispersal, and (2) facilitation of seedling establishment in the vicinity of grass tussocks in vegetation gaps was a more realistic representation of field observations realised, with rosettes of H. pilosella grown from seeds occasionally distributed within dense grass vegetation. Phenotypic plasticity of stolon length was a decisive factor for the maintenance of H. pilosella populations. We conclude that a mixed strategy of clonal growth and reproduction by seeds in H. pilosella is necessary to maintain populations of this species in the presence of high interspecific competition and a shortage of open space.

Algorithms↗

PubMed2002

Competition and species packing in patchy environments.

In models of competition in which space is treated as a continuum, and population size as continuous, there are no limits to the number of species that can coexist. For a finite number of sites, N, the results are different. The answer will, of course, depend on the model used to ask the question. In the Tilman-May-Nowak ordinary differential equation model, the number of species is asymptotically C log N with most species packed in at the upper end of the competitive hierarchy. In contrast, for metapopulation models with discrete individuals and stochastic spatial systems with various competition neighborhoods, we find a traditional species area relationship CN(a), with no species clumping along the phenotypic gradient. The exponent a is larger by a factor of 2 for spatially explicit models. In words, a spatial distribution of competitors allows for greater diversity than a metapopulation model due to the effects of recruitment limitation in their competition.

Competitive Behavior↗