Individual-based Simulation Model Research Articles

Understanding soaring bird migration through interactions and decisions at the individual level

Many soaring bird species migrate southwards in autumn from their breeding grounds in Europe and Central Asia towards their wintering grounds. Our knowledge about interactions between migrating birds, thermal selection during migration and mechanisms that lead to flocking or convergent travel networks is still very limited. To start investigating these aspects we developed an individual-based simulation model that describes the local interactions between birds and their environment during their migratory flight, leading to emergent patterns at larger scales. The aim of our model is to identify likely decision rules with respect to thermal selection and navigation. After explaining the model, it is applied to analyse the migration of white storks (Ciconia ciconia) over part of its migration domain. A model base-run is accompanied by a sensitivity analysis. It appears that social interactions lead to the use of fewer thermals and slight increases in distance travelled. Possibilities for different model extensions and further model application are discussed.

Long-term ecological impacts of clear-fell logging on tree species diversity in a subtropical forest, southern Japan

Defining the spatial arrangement and length of the cutting cycle in a logged area is crucial for reconciling potential conflicts between timber yields and maintenance of ecosystem services in natural forests. In this study, we investigated long-term impacts of clear-fell logging on timber production and tree species diversity in a subtropical forest on the Ryukyu Islands, using an individual-based simulation model. We assumed six logging scenarios defined by combinations of forest type and regeneration processes, which acted as surrogates for spatial scales of clear-fell logging. These scenarios were simulated under cutting cycles ranging from 20 to 150 years. Short-cutting cycles resulted in dominance by the sprouting species Castanopsis sieboldii. The compositional shift was accelerated by the lack of seed dispersal from surrounding forest areas. The simulations demonstrated that a sustainable logging regime maintaining both yield and tree species diversity requires a cutting cycle longer than 50 years. The simulation results also suggest that the trade-off between the recovery of tree species diversity and timber production is favored more in stands surrounded by mature forest than in isolated stands or stands surrounded by immature forest. Ecological risk assessments based on model simulations provide an alternative to current forest management practices that rely on empirical knowledge.

An integration of habitat evaluation, individual based modeling, and graph theory for a potential black bear population recovery in southeastern Texas, USA

Population recovery is difficult for species that require large contiguous areas of habitat, particularly within areas of heterogeneous land ownerships. Ecologically, potential for recovery success requires assessment of quantity, quality, and distribution of available habitat. Our objective was to evaluate habitat for a possible Louisiana black bear recovery in southeastern Texas. First, we categorized land cover and identified remote areas of highly suitable habitat. Next, we used the individual based simulation model J-walk to estimate ability of female black bears to move among remote habitat patches. Then, we applied graph theory to J-walk output to evaluate overall connectivity of remote habitat. An estimated 225,626 ha of remote habitat were identified in 901 patches, most of which was located within the eastern half of the study area. Network analysis showed specific areas where targeted conservation efforts may help black bear population expansion throughout the study region. Ultimately, enough habitat area exists to sustain a black bear population and it is best connected among public and private lands largely within the eastern half of the study area. Habitat evaluation will need to be revisited if black bears establish themselves locally and actual habitat use data become available. Regardless, our analysis demonstrates an important first step that may be incorporated into a larger adaptive management framework, updated, and replicated as more-detailed habitat suitability and land use data are available.

Reducing Plasmodium falciparum Malaria Transmission in Africa: A Model-Based Evaluation of Intervention Strategies

BackgroundOver the past decade malaria intervention coverage has been scaled up across Africa. However, it remains unclear what overall reduction in transmission is achievable using currently available tools.Methods and FindingsWe developed an individual-based simulation model for Plasmodium falciparum transmission in an African context incorporating the three major vector species (Anopheles gambiae s.s., An. arabiensis, and An. funestus) with parameters obtained by fitting to parasite prevalence data from 34 transmission settings across Africa. We incorporated the effect of the switch to artemisinin-combination therapy (ACT) and increasing coverage of long-lasting insecticide treated nets (LLINs) from the year 2000 onwards. We then explored the impact on transmission of continued roll-out of LLINs, additional rounds of indoor residual spraying (IRS), mass screening and treatment (MSAT), and a future RTS,S/AS01 vaccine in six representative settings with varying transmission intensity (as summarized by the annual entomological inoculation rate, EIR: 1 setting with low, 3 with moderate, and 2 with high EIRs), vector–species combinations, and patterns of seasonality. In all settings we considered a realistic target of 80% coverage of interventions. In the low-transmission setting (EIR∼3 ibppy [infectious bites per person per year]), LLINs have the potential to reduce malaria transmission to low levels (<1% parasite prevalence in all age-groups) provided usage levels are high and sustained. In two of the moderate-transmission settings (EIR∼43 and 81 ibppy), additional rounds of IRS with DDT coupled with MSAT could drive parasite prevalence below a 1% threshold. However, in the third (EIR = 46) with An. arabiensis prevailing, these interventions are insufficient to reach this threshold. In both high-transmission settings (EIR∼586 and 675 ibppy), either unrealistically high coverage levels (>90%) or novel tools and/or substantial social improvements will be required, although considerable reductions in prevalence can be achieved with existing tools and realistic coverage levels.ConclusionsInterventions using current tools can result in major reductions in P. falciparum malaria transmission and the associated disease burden in Africa. Reduction to the 1% parasite prevalence threshold is possible in low- to moderate-transmission settings when vectors are primarily endophilic (indoor-resting), provided a comprehensive and sustained intervention program is achieved through roll-out of interventions. In high-transmission settings and those in which vectors are mainly exophilic (outdoor-resting), additional new tools that target exophagic (outdoor-biting), exophilic, and partly zoophagic mosquitoes will be required. Please see later in the article for the Editors' Summary

Developing guidelines for school closure interventions to be used during a future influenza pandemic

BackgroundThe A/H1N1 2009 influenza pandemic revealed that operational issues of school closure interventions, such as when school closure should be initiated (activation trigger), how long schools should be closed (duration) and what type of school closure should be adopted, varied greatly between and within countries. Computer simulation can be used to examine school closure intervention strategies in order to inform public health authorities as they refine school closure guidelines in light of experience with the A/H1N1 2009 pandemic.MethodsAn individual-based simulation model was used to investigate the effectiveness of school closure interventions for influenza pandemics with R0 of 1.5, 2.0 and 2.5. The effectiveness of individual school closure and simultaneous school closure were analyzed for 2, 4 and 8 weeks closure duration, with a daily diagnosed case based intervention activation trigger scheme. The effectiveness of combining antiviral drug treatment and household prophyaxis with school closure was also investigated.ResultsIllness attack rate was reduced from 33% to 19% (14% reduction in overall attack rate) by 8 weeks school closure activating at 30 daily diagnosed cases in the community for an influenza pandemic with R0 = 1.5; when combined with antivirals a 19% (from 33% to 14%) reduction in attack rate was obtained. For R0 >= 2.0, school closure would be less effective. An 8 weeks school closure strategy gives 9% (from 50% to 41%) and 4% (from 59% to 55%) reduction in attack rate for R0 = 2.0 and 2.5 respectively; however, school closure plus antivirals would give a significant reduction (~15%) in over all attack rate. The results also suggest that an individual school closure strategy would be more effective than simultaneous school closure.ConclusionsOur results indicate that the particular school closure strategy to be adopted depends both on the disease severity, which will determine the duration of school closure deemed acceptable, and its transmissibility. For epidemics with a low transmissibility (R0 < 2.0) and/or mild severity, individual school closures should begin once a daily community case count is exceeded. For a severe, highly transmissible epidemic (R0 >= 2.0), long duration school closure should begin as soon as possible and be combined with other interventions.

First Lagrangian ROMS–IBM simulations indicate large losses of chokka squid Loligo reynaudii paralarvae from South Africa's Agulhas Bank

Present knowledge of ocean currents based on in situ observation and models suggests that passive biological material such as eggs and larvae can be advected offshore away from the Agulhas Bank, South Africa, and hence removed from the ecosystem on which their survival and recruitment depends. Such losses have been cited as the root cause of the sudden drop in annual squid catches experienced in 2001. In this study, a Lagrangian IBM (individual-based model) coupled to a ROMS (regional ocean model system) model was used to investigate this hypothesis. Three simulations were performed for 12 model months using neutrally buoyant particles released from the seabed (120 m) every second day on the mid-shelf of the eastern, central and western regions of the Agulhas Bank. Boundary effects and resolution precluded the release of virtual particles on the inshore spawning grounds. Particles were given lifespans of 40 days. Results demonstrated large particle losses from the eastern Agulhas Bank (76%) and the western Agulhas Bank (64%). In contrast, few particles were lost from the central Agulhas Bank (2%), making this, in terms of the model, the most suitable place on the Agulhas Bank for spawning. Visualisation of the ROMS outputs revealed that leakage on the eastern Agulhas Bank was caused by a cyclonic eddy resident in the Agulhas Bight. Similarly, leakage from the western Agulhas Bank was caused by deep-water cyclonic eddies in the adjacent Atlantic Ocean.

Individual-based simulation of sexual selection: A quantitative genetic approach

Sexual selection has been mathematically modeled using quantitative genetics as well as population genetics. Two-locus simulation models have been used to study the evolution of male display and female preference. We present an individual-based simulation model of sexual selection in a quantitative genetic context. We show that under certain conditions Fisherian self-reinforcing sexual selection takes effect, predicted by Lande’s analytic model of female choice. We also show that the dynamics involved in the co-evolution of male display and female preference is much more complex than mathematics would predict. We therefore argue that the study of sexual selection through individual-based simulation could give new and more realistic insight into a world dominated by overly simplified equations.

Restoration thinning accelerates structural development and carbon sequestration in an endangered Australian ecosystem

1. Restoration thinning involves the selective removal of stems in woody ecosystems to restore historical or ecologically desirable ecosystem structure and processes. Thinning may also accelerate carbon sequestration in dense regenerating forests. This study considers restoration thinning effects on both structural development and carbon sequestration in a regenerating forest ecosystem. 2. An experimental thinning trial was established in dense Acacia harpophylla regrowth in southern Queensland, Australia. The mean stem density prior to thinning was 17 000 stems ha−1. Four treatments (no thinning and thinning down to 1000, 2000 and 4000 stems ha−1) were applied in a randomized block design. Growth and mortality of a subset of stems was monitored for 2 years. Mixed-effects models and hierarchical Bayesian models (HBMs) were used to test for treatment effects and to explore relationships between neighbourhood density variables and the growth and mortality of stems. The HBMs were subsequently used to parameterise an individual-based simulation model of stand structural development and biomass accumulation over 50 years. 3. The circumference growth rates of stems in thinning treatments were significantly higher than in the control. Woody species diversity and grass cover were also significantly higher in thinning treatments and were strongly negatively correlated with canopy cover. The HBMs confirmed that both growth and mortality were density dependent to some extent. 4. The simulation model predicted a net gain in living above-ground biomass in some thinning treatments (compared with the control treatment) within 20 years after thinning. The 6000 stems ha−1 treatment was predicted to be the optimal thinning density for structural development towards the structure of a nearby mature reference forest. 5. Synthesis and applications. Naturally regenerating woody vegetation provides important habitat for native fauna in fragmented landscapes and represents an efficient means to reinstate habitat connectivity and increase forest area. Many regrowth ecosystems also have considerable potential as land-based carbon sinks. This study demonstrates that restoration thinning can be applied to accelerate stem growth and woody species recruitment and may also accelerate structural development and carbon sequestration in this extensive regrowth ecosystem. The application of restoration thinning to provide dual restoration and carbon benefits should be explored for a wider range of naturally regenerating woody ecosystems.

Evolution of avian clutch size along latitudinal gradients: do seasonality, nest predation or breeding season length matter?

Birds display a latitudinal gradient in clutch size with smaller clutches in the tropics and larger in the temperate region. Three factors have been proposed to affect this pattern: seasonality of resources (SR), nest predation and length of the breeding season (LBS). Here, we test the importance of these factors by modelling clutch size evolution within bird populations under different environmental settings. We use an individual-based ecogenetic simulation model that combines principles from population ecology and life history theory. Results suggest that increasing SR from the tropics to the poles by itself or in combination with a decreasing predation rate and LBS can generate the latitudinal gradient in clutch size. Annual fecundity increases and annual adult survival rate decreases from the tropics to the poles. We further show that the annual number of breeding attempts that (together with clutch size) determines total annual egg production is an important trait to understand latitudinal patterns in these life history characteristics. Field experiments that manipulate environmental factors have to record effects not only on clutch size, but also on annual number of breeding attempts. We use our model to predict the outcome of such experiments under different environmental settings.

On the evolution of cell size distribution during bacterial growth cycle: Experimental observations and individual-based model simulations

Individual-based modelling (IbM) has become a fully incorporated part of predictive microbiology methodologies in the last decade. Previous studies of bacterial culture growth cycle with the IbM simulator INDISIM analysed the evolution of bacterial biomass distribution during the different phases of growth. The predicted forward shift during lag, stability during exponential and backward shift when entering the stationary phase have been experimentally observed in an

Lognormal distribution of individual lifetime fecundity: insights from a 23‐year study

Individual variance in lifetime fecundity within populations is a life-history parameter of crucial evolutionary and ecological significance. However, knowledge of its magnitude and underlying mechanisms in natural populations is biased toward short-lived taxa. This paper summarizes results of a 23-year study on a population of the Mediterranean shrub Lavandula latifolia. We document the within-population pattern of individual variation in instantaneous and lifetime fecundity (as estimated by inflorescence production) and explore the mechanisms producing the lognormal distribution of individual fecundities by means of an individual-based simulation model. Throughout the study period, a few individuals consistently produced most inflorescences while the majority of plants exhibited moderate-to-low fecundities. The shape of yearly distributions of annual fecundities varied little across years, and most annual fecundity distributions did not depart significantly from a lognormal. The distribution of individual lifetime fecundity did not depart from lognormality. Despite the simplicity of the premises of our simulation model, it was remarkably successful at predicting the shapes of fecundity distributions and the early establishment of a persistent fecundity hierarchy. The agreement between model results and empirical data supports the view that multiplicative interactions of randomly varying environmental effects can play a central role in determining individual variation in lifetime fecundity in L. latifolia, and suggests that environmental stochasticity can be decisive in the genesis of strong fecundity hierarchies in long-lived plants.

Bet-hedging as an evolutionary game: the trade-off between egg size and number

In a recent paper, [Olofsson et al . (2009)][1] explore the evolution of egg mass in a temporally variable environment using an individual-based simulation model. The model includes realistic assumptions such as density-dependent population growth and a fluctuating minimum size for survival. Their

Spatial distribution of flower vs. honeydew resources in cereal fields may affect aphid parasitism

The potential impact of nectar availability for biological pest control is of increasing relevance due to the disappearance of non-crop plants in intensified agricultural landscapes. However, little is known about how floral resources and their spatial distribution in and around crop fields influence cereal aphid parasitoid (Hymenoptera, Aphidiidae) survival and population dynamics. Cereal aphid parasitoids may be less dependent on flowers as they can use honeydew from their aphid hosts as an alternative food resource. However, honeydew appears to be less suitable as a food source for parasitoids when compared to nectar. Here the effects of flower distribution (nectar), aphid abundance (honeydew quantity) and honeydew quality on parasitoid life history parameters were explored using a spatially explicit, individual-based simulation model. In addition, effects of the availability of floral resources in field margins on parasitism levels in winter wheat were investigated in a field study. In the simulation study three flower distributions were compared: (i) flowers restricted to the field margin (most common in agricultural landscapes) or (ii) flowers in strips within the crop, and (iii) random flower distribution in the field. Simulations suggest that nectar feeding increases parasitoid longevity and parasitism at low aphid densities, but only in fields with randomly distributed flowers. In contrast, the spatial distribution of flowers did not affect the parasitoid longevity and parasitism rate at high aphid densities, where parasitoid feeding was restricted to the abundant honeydew resources. In simulations, parasitoid survival and the number of aphids parasitized were also affected by the nutritional quality of the honeydew, with low quality honeydew having a less positive effect on parasitoid longevity and parasitism rate. The field study did not indicate evidence of a significant relationship between flower cover in field margins and parasitism rates in wheat near the margins. This finding is compatible with results from simulations and suggests that honeydew feeding is more prevalent in cereal aphid parasitoids than nectar feeding. In conclusion, nectar may be an important factor for the potential biocontrol success of cereal aphid parasitoids, but most likely only at low aphid densities and especially when flowers are broadly distributed in the field.

Bacteria can form interconnected microcolonies when a self-excreted product reduces their surface motility: evidence from individual-based model simulations

Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations, we suggest a mechanism that could be responsible for these interconnected microcolonies.

Incorporating behaviour into simple models of dispersal using the biological control agent Dicyphus hesperus

We explored the utility of incorporating easily measured, biologically realistic movement rules into simple models of dispersal. We depart from traditional random walk models by designing an individual-based simulation model where we decompose animal movement into three separate processes: emigration, between-patch movement, and immigration behaviour. These processes were quantified using experiments on the omnivorous insect Dicyphus hesperus moving through a tomato greenhouse. We compare the predictions of the individual-based model, along with a series of biased random walk models, against an independent experimental release of D. hesperus. We find that in this system, the short-term dispersal of these insects is described well by our individual-based model, but can also be described by a 2D grid-based biased random walk model when mortality is accounted for.

Habitat conversion, extinction thresholds, and pollination services in agroecosystems

Parallel declines of wild pollinators and pollinator-dependent plants have raised alarms over the loss of pollination services in agroecosystems. A spatially explicit approach is needed to develop specific recommendations regarding the design of agricultural landscapes to sustain wild pollinator communities and the services they provide. I modeled pollination services in agroecosystems using a pair of models: a stochastic individual-based simulation model of wild pollinators, pollinator-dependent plants, and crop pollination; and a set of coupled difference equations designed to capture the nonspatial component of the simulation model. Five spatially explicit models of habitat conversion to crops were simulated, and results for pollination services were compared. Mean-field behavior of the simulation model was in good agreement with analysis of the difference equations. A major feature of the models was the presence of a cusp leading to loss of stability and extinction of pollinators and pollinator-dependent plants beyond a critical amount of habitat loss. The addition of pollen obtained from crop visitation caused a breakdown of the cusp preventing extinction of pollinators, but not of wild pollinator-dependent plants. Spatially restricted foraging and dispersal also altered model outcomes relative to mean-field predictions, in some cases causing extinction under parameter settings that would otherwise lead to persistence. Different patterns of habitat conversion to crops resulted in different levels of pollination services. Most interesting was the finding that optimal pollination services occurred when the size of remnant habitat patches was equal to half the mean foraging and dispersal distance of pollinators and the spacing between remnant patches was equal to the mean foraging and dispersal distance. Conservation of wild pollinators and pollinator-dependent plants in agroecosystems requires careful attention to thresholds in habitat conversion and spatial pattern and scale of remnant habitats. Maximization of pollination services was generally incompatible with conservation of wild pollinator-dependent plants. My prediction is that pollination services will be maximized by providing islands of nesting habitat where interisland distance matches mean foraging distances of wild pollinators.

The power of simulating experiments

Addressing complex ecological research questions often requires complex empirical experiments. However, due to the logistic constraints of empirical studies there is a trade-off between the complexity of experimental designs and sample size. Here, we explore if the simulation of complex ecological experiments including stochasticity-induced variation can aid in alleviating the sample size limitation of empirical studies. One area where sample size limitations constrain empirical approaches is in studies of the above- and belowground controls of trophic structure. Based on a rule- and individual-based simulation model on the effect of above- and belowground herbivores and their enemies on plant biomass, we evaluate the reliability of biomass estimates, the probability of experimental failure in terms of missing values, and the statistical power of biomass comparisons for a range of sample sizes. As expected, we observed superior performance of setups with sample sizes typical of simulations ( n = 1000) as compared to empirical experiments ( n = 10). At low sample sizes, simulated standard errors were smaller than expected from statistical theory, indicating that stochastic simulation models may be required in those cases where it is not possible to perform pilot studies for determining sample sizes. To avoid experimental failure, a sample size of n = 30 was required. In conclusion, we propose that the standard tool box of any ecologist should comprise a combination of simulation and empirical approaches to benefit from the realism of empirical experiments as well as the statistical power of simulations.

Dense and sparse aggregations in complex motion: Video coupled with simulation modeling

Investigations into the complex behaviors of aggregations of highly mobile animals have not used the link between image processing technology and simulation modeling fruitfully to address many fundamental ecological issues. Examples include population censusing, which remains difficult despite the demonstrated ecological importance of assessing abundance and density of organisms. We introduce a theoretical framework that connects thermal infrared video imaging with an individual-based simulation model—an approach that appears to be applicable to a diverse set of aggregated, highly mobile, nocturnal animals. To demonstrate the framework two applications are presented. The first is a dense aggregation of Brazilian free-tailed bats ( Tadarida brasiliensis) that exhibits an emergence pattern that has complex dynamics and the second is a sparse local aggregation of agricultural pest moths whose dynamics are insipid. The first application uses individual-based modeling to mimic the behavior in the video of bats during a nightly emergence from a cave and to provide reliable estimates of the numbers, and associated error bounds. The second application uses video recordings of sparse aggregations to provide consistent estimates of the numbers of flying noctuid moths recorded over a corn and cotton-dominated agroecosystem in south-central Texas. This does not use a mathematical model because error estimates tend to be small.

Evolution of body condition‐dependent dispersal in metapopulations

Body condition-dependent dispersal strategies are common in nature. Although it is obvious that environmental constraints may induce a positive relationship between body condition and dispersal, it is not clear whether positive body conditional dispersal strategies may evolve as a strategy in metapopulations. We have developed an individual-based simulation model to investigate how body condition-dispersal reaction norms evolve in metapopulations that are characterized by different levels of environmental stochasticity and dispersal mortality. In the model, body condition is related to fecundity and determined either by environmental conditions during juvenile development (adult dispersal) or by those experienced by the mother (natal dispersal). Evolutionarily stable reaction norms strongly depend on metapopulation conditions: positive body condition dependency of dispersal evolved in metapopulation conditions with low levels of dispersal mortality and high levels of environmental stochasticity. Negative body condition-dependent dispersal evolved in metapopulations with high dispersal mortality and low environmental stochasticity. The latter strategy is responsible for higher dispersal rates under kin competition when dispersal decisions are based on body condition reached at the adult life stage. The evolution of both positive and negative body condition-dependent dispersal strategies is consequently likely in metapopulations and depends on the prevalent environmental conditions.

Can fertility signals lead to quality signals? Insights from the evolution of primate sexual swellings.

The sexual swellings of female primates have generated a great deal of interest in evolutionary biology. Two hypotheses recently proposed to elucidate their functional significance argue that maximal swelling size advertises either female fertility within a cycle or female quality across cycles. Published evidence favours the first hypothesis, and further indicates that larger swellings advertise higher fertility between cycles. If so, a male preference for large swellings might evolve, driving females to use swellings as quality indicators, as proposed by the second hypothesis. In this paper, we explore this possibility using a combination of empirical field data and mathematical modelling. We first test and find support for three key predictions of the female-quality hypothesis in wild chacma baboons (Papio ursinus): (i) inter-individual differences in swelling size are maintained across consecutive cycles, (ii) females in better condition have larger swellings and higher reproductive success, and (iii) males preferentially choose females with large swellings. We then develop an individual-based simulation model that indicates that females producing larger swellings can achieve higher mating success even when female-female competition is low and within-female variance in the trait is high. Taken together, our findings show that once sexual swellings have evolved as fertility signals, they might, in certain socio-sexual systems, be further selected to act as quality signals. These results, by reconciling two hypotheses, help to clarify the processes underlying sexual swelling evolution. More generally, our findings suggest that mate choice for direct benefits (fertility) can lead to indirect benefits (good genes).