Adaptive search in juvenile plaice foraging for aggregated and dispersed prey

Juvenile plaice Pleuronectes platessa in a laboratory arena used intensive search behaviour, characterized by short movements and frequent turning, in the five movements before and after attacking a prey in an aggregated distribution. They used extensive search behaviour with, on average, longer movements and less turning at all other times. Intensive search was, apparently, triggered by a high local density of prey but not by isolated prey. This response to local prey density resulted in area-restricted search when prey were aggregated and win-shift behaviour when prey were dispersed. There was no evidence that the use of intensive search increased with experience of aggregated prey. It therefore appears that the fish were able to exploit encountered prey distribution patterns using their immediate perceptions rather than prior experience.     

SMOES: a simulation model for the Oosterschelde ecosystem

The model SMOES integrates the results of the ecological research program conducted in the Oosterschelde estuary before and during the construction of a storm surge barrier. Its aim is to provide a quantitative summary of the research findings and to provide a tool for analysis and prediction of the ecosystem in response to human manipulations. This chapter describes model background and formulations. An uncertainty analysis is used to analyze the effect of uncertainties in model parameters on model outcome. The results of the sensitivity analysis are classified by distinguishing groups of model parameters with a qualitatively different effect on model results. Within these groups, a quantitative ranking of the parameters is possible. It appears that the most sensitive parameters represent processes that are relatively little studied in the Oosterschelde, which may provide guidelines for further research.     

Experiments and a model examining learning in the area-restricted search behavior of ferrets (Mustela putorius furo)

Area-restricted searches have been described as important componentsof the foraging behavior of many organisms. It is unclear, however,whether individual foragers can use learning to fine-tune theirsearches, or even whether these searches are efficiently performed.I used a simulation model to make qualitative predictions aboutsearch behavior in a laboratory system. The simulation modelindicates that the sinuosity and path length of searches stronglyaffect search efficiency. The model predicts that, for a rate-maximizingforager, path length should increase and search sinuosity shoulddecrease as prey become less clumped. Foraging animals may thereforebe selected to learn the path length and sinuosity of searchesin response to changing degrees of dumping of prey. These predictionswere tested in a laboratory system involving ferrets (Mustelaputorius furo) foraging for oil-drop "prey items." Search pathschanged in a graded manner to experimental manipulations ofthe dumping of prey. As predicted by the model, ferrets learnedto perform longer and less sinuous search paths as prey becameless clumped. This study provides the first evidence that area-restrictedsearch behavior is learned and can be fine-tuned to efficientlyexploit different spatial distributions of food.     

Prey capture tactics of spiders: An analysis based on a simulation model for spider's growth

The prey capture tactics of spiders was analyzed, considering the energy gained by the capture of prey and that required for it. For the purpose of it, a growth model of spiders was constructed, expressing the flow rate of prey biomass to the spider's body by differential equations. Solving these equations under the differing values of three parameters, growth curves of spiders was obtained. These three parameters are the amount of prey biomass supplied daily to spiders, x₀, the rate of prey capture of spiders, α, and a coefficient of the respiration rate required for the capture of prey, k. When the value of k increased, spiders could grow only at high value of x₀. These results suggest that habitats with small prey biomass are preferred by spiders adopting a sit-and-wait tactics for prey capture, which requires small values of k. Wolf spiders are one of these spiders showing that tactics. On the other hand, web-builders which require large amount of energy for spinning webs (namely, take large value of k), are able to grow only in the habitats with large prey biomass. Each species of spiders are considered to locate in a certain point between both extremes of these tactics for the capture of prey.     

The effect of prey type and density on the foraging efficiency of juvenile perch, (Perca fluviatilis)

The foraging efficiency of juvenile perch (Perca fluviatilis), feeding on two types of prey, was studied in laboratory experiments. Waterfleas (Daphnia magna) and phantom midge larvae (Chaoborus flavicans) were offered in a range of densities, either separately or combined. Perch fed more efficiently on each prey type separately than when both were mixed. Foraging efficiency decreased with an increase of mixed prey density with both prey types present in equal numbers, but also when the proportion of Chaoborus increased. This could be caused by the existence of different hunting techniques, each of which is fully efficient in the presence of one prey type only. In the presence of two prey types, the predator constantly has to switch from one hunting technique to another.     

The local enhancement conundrum: In search of the adaptive value of a social learning mechanism

Social learning mechanisms are widely thought to vary in their degree of complexity as well as in their prevalence in the natural world. While learning the properties of a stimulus that generalize to similar stimuli at other locations (stimulus enhancement) prima facie appears more useful to an animal than learning about a specific stimulus at a specific location (local enhancement), empirical evidence suggests that the latter is much more widespread in nature. Simulating populations engaged in a producer–scrounger game, we sought to deploy mathematical models to identify the adaptive benefits of reliance on local enhancement and/or stimulus enhancement, and the alternative conditions favoring their evolution. Surprisingly, we found that while stimulus enhancement readily evolves, local enhancement is advantageous only under highly restricted conditions: when generalization of information was made unreliable or when error in social learning was high. Our results generate a conundrum over how seemingly conflicting empirical and theoretical findings can be reconciled. Perhaps the prevalence of local enhancement in nature is due to stimulus enhancement costs independent of the learning task itself (e.g. predation risk), perhaps natural habitats are often characterized by unreliable yet highly rewarding payoffs, or perhaps local enhancement occurs less frequently, and stimulus enhancement more frequently, than widely believed.     

The effect of prey density on foraging mode selection in juvenile lumpfish: balancing food intake with the metabolic cost of foraging

1. In many species, individuals will alter their foraging strategy in response to changes in prey density. However, previous work has shown that prey density has differing effects on the foraging mode decisions of ectotherms as compared with endotherms. This is likely due to differences in metabolic demand; however, the relationship between metabolism and foraging mode choice in ectotherms has not been thoroughly studied. 2. Juvenile lumpfish Cyclopterus lumpus forage using one of two modes: they can actively search for prey while swimming, or they can 'sit-and-wait' for prey while clinging to the substrate using a ventral adhesive disk. The presence of these easily distinguishable foraging modes makes juvenile lumpfish ideal for the study of foraging mode choice in ectotherms. 3. Behavioural observations conducted during laboratory experiments showed that juvenile lumpfish predominantly use the 'cling' foraging mode when prey is abundant, but resort to the more costly 'swim' mode to seek out food when prey is scarce. The metabolic cost of active foraging was also quantified for juvenile lumpfish using swim-tunnel respirometry, and a model was devised to predict the prey density at which lumpfish should switch between the swim and cling foraging modes to maximize energy intake. 4. The results of this model do not agree with previous observations of lumpfish behaviour, and thus it appears that juvenile lumpfish do not try to maximize their net energetic gain. Instead, our data suggest that juvenile lumpfish forage in a manner that reduces activity and conserves space in their limited aerobic scope. This behavioural flexibility is of great benefit to this species, as it allows young individuals to divert energy towards growth as opposed to activity. In a broader context, our results support previous speculation that ectotherms often forage in a manner that maintains a minimum prey encounter rate, but does not necessarily maximize net energy gain.     

像元尺度上不确定性对空间景观直观模型模拟的影响

LANDIS模型是模拟自然和人为干扰下森林景观变化的空间直观景观模型。模型把景观概念化为由相同大小的像元或样地组成的格网。在每一个像元上,模型要求输入物种和年龄组信息。但是,由于研究区一般由成千上百万个像元构成,不可能通过实际调查获取每一个像元上的物种和年龄组信息。因此,采用了一种基于小班的随机赋值法从森林调查数据中获取每一个像元的物种和年龄组信息。该方法是一种基于概率的方法,会在LANDIS模型模拟的物种和年龄组信息的输入中引入不确定性。为了评价由基于小班的随机赋值法所引入像元尺度上的不确定性对模型模拟结果的影响,用蒙特卡罗模拟法进行不确定性分析。对LANDIS模型模拟的每一个物种,用众数年龄组发生频率来定量化单个像元上年龄组信息的不确定性,用所有像元上的众数年龄组平均发生频率来定量化年龄组信息在像元尺度上总的不确定性。平均发生频率越高,不确定性越低。为了评价基于小班的随机赋值法对景观尺度上模型模拟结果的影响,计算了每一个物种在整个研究区内的面积百分比和聚集度指数。变异系数越大,不确定性越高。对所有物种,年龄组信息不确定性在模型模拟的初期是比较低的(平均发生频率大于10)。种子传播、建群、死亡和火干扰使模型结果的不确定性随模拟时间增加而增加。最后,不确定性达到稳定状态,达到平衡状态的时间与物种寿命接近。此时,初始的物种和年龄组信息不再对模型结果有影响。在景观尺度上,物种分布面积百分比和由聚集度指数所定量化的空间格局并未受像元尺度上不确定性增加的影响。因为LANDIS模型模拟研究的目的在于预测总的景观格局变化,而不是单一的事件,所以,基于小班的随机赋值法可用于LANDIS模型的参数化。     

The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model

Abstract

The capacity of silencing genes makes small interfering RNA (siRNA) becomes potential candidates for curing many fatal diseases. Due to the low stability and delivery efficiency of siRNA, the design of amphiphilic carrier for siRNA delivery is vital for the practical gene therapy. In the present work, we explored how the complexation and dissociation of siRNA with poly (maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine (PMAL), which is a recent synthesised amphiphilic polymer and can be used in delivery of siRNAs and proteins, using traditional molecular dynamics simulations, together with steered molecular dynamics simulations. It was shown that the complexation of siRNA with PMALs can spontaneously occur, no matter what unit number of PMAL is. PMALs of different unit numbers form micelle-like structures and interact with siRNA surface. With the increase of unit number, PMAL becomes more flexible and interacts with siRNA from attachment to entanglement. The dissociation of PMAL from siRNA is an energy-consuming process. The free energy difference increases with the unit number of PMAL. The free energy for dissociation involves both the stretch of PMAL and the separation of PMAL from siRNA. Therefore, an optimal unit number of PMAL is critical for the delivery efficiency of siRNA when PMAL is used as carrier. In present work, when the radius of gyration of PMAL approaches to that of siRNA, PMAL gives a favoured both complexation and dissociation between siRNA and PMAL. Finally, we propose the mechanism of complexation and dissociation of PMAL with siRNA. The above simulation established a molecular insight of the interaction between siRNA and PMAL and was helpful for the design and applications of new PMAL-based polymers as siRNA delivery carriers.     

The blind leading the blind in army ant raid patterns: Testing a model of self-organization (Hymenoptera: Formicidae)

We present field experiments and analyses that test both the assumptions and the predictions of a model that showed how the swarm raids of the army ant Eciton burchellimight be self-organizing, i.e., based on hundreds of thousands of interactions among the foraging workers rather than a central administration or hierarchical control. We use circular mill experiments to show that the running velocity of the ants is a sigmoidal function of the strength of their trail pheromones and provide evidence that the swarm raid is structured by the interaction between outbound and inbound forager traffic mediated by the pheromones produced by both of these sets of ants. Inbound traffic is also affected by the distribution of prey, and hence, sites of prey capture alter the geometry of the raid. By manipulating the prey distributions for E. burchelliswarms, we have made them raid in a form more typical of other army ant species. Such self-organization of raids based on an interaction between the ants and their environment has profound consequences for interpretations of the evolution of army ant species.     

A simulation model for the fate of pesticide residues in a field soil

The model employed for simulating the fate of pesticides in soil was based on the one dimensional convective-dispersive-reaction equation. The model assumed a constant pore-water velocity (v), linear equilibrium adsorption, and first-order degradation. The adsorption parameter (k_d) was calculated from molecular structure with the help of a first-order molecular connectivity index. On the basis of the results of sensitivity analysis the model was made partially stochastic in order to account for horizontal heterogenity in a field soil. Concentration profiles were obtained by employing the mode, median and mean values of (v, D) while the values of k_d and t_1/2 were kept constants; where D and t_1/2 were the apparent diffusion coefficient and the degradation half-life, respectively. The resulted extremes in concentration profiles were expected to be observed within a relatively small area of the heterogeneous filed soil. A random variable, namely the contaminated depth, was defined so that the soil beneath it would be practically free of pesticide during its entire life-time. The values of (₁, ₂, ₃) under continuous leaching were (0.14, 0.56, 1.00 m), (0.29, 1.50, 2.62 m), and (0.65, 2.25, 4.00m) for DDT, toxaphene and lindane, respectively; where ₁, ₂ and ₃ were values of calculated by employing the mode, median, and mean values of (v, D), respectively. Within a relatively small area the first value would be frequently observed whereas the others would be less pronounced. The depth and shape of the resultant base of the contaminated zone were substantially more sensitive to changes in the surface rates of recharge than to changes in the values of the chemical parameters k_d and t_1/2. The implication of the results for the assesment of pesticide contamination of groundwaters were discussed.     

How landscapes affect the evolution of dispersal behaviour in reef fishes: results from an individual‐based model

The vast majority of tropical reef fishes have a sedentary adult phase and pelagic larval phase that is potentially highly dispersive. Dispersal may be favoured by a wide range of factors including the arrangement of suitable habitat in space. In this paper the dispersal strategy of individuals is followed and allowed to evolve in a simplified model of three different landscapes: an enclosed sea, an open archipelago and a barrier reef. The three landscapes have very different characteristics, but all have similar spatial clumping of reef habitat. In all landscapes, as minimum time to settlement increases, evolved movement strategy also increases and longer settlement windows favour dispersal. In the archipelago movement is not maximized until the minimum pelagic duration is longer than in the other landscapes. The model predicts that, given the same pelagic duration, species from enclosed seas should have more dispersive behaviours than those from open archipelagos, because of the density of habitat and the aggregation of habitat in space affect the likelihood of larvae finding suitable habitat for settlement.     

基于智能体模型的青岛市林地生态格局评价与优化

设计并在GIS平台上开发了基于智能体的生态格局评价模型,以青岛市及周边地区林地为研究对象,分析不同林地空间格局及生态网络保护框架对于物种生存与扩散的影响.结果表明,与现状相比,不同等级的生态网络框架对物种种群数量与物种迁移都有明显提升,且等级越高的生态网络框架提升作用越明显.然而仅仅依靠生态网络框架不足以使研究区域林地系统形成功能上的相互连通,因此,在分析研究区域现状土地利用格局基础上,提出与湿地系统结合,在胶州湾周围及大沽河干流地区增加林地的空间布局.通过模型模拟分析,发现优化后的林地空间格局结合生态网络框架能有效提升林地之间的物种扩散.基于模拟结果,为研究区林地生态格局构建提出如下建议:(1)保证现有的规模较大的林地不被破坏;(2)青岛市中部湿地系统可以作为新增林地的理想区域;(3)生态网络框架可作为青岛市建立城市组团间生态间隔的空间参考.     

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

The aspartate‐derived amino‐acid pathway from plants is well suited for analysing the function of the allosteric network of interactions in branched pathways. For this purpose, a detailed kinetic model of the system in the plant model Arabidopsis was constructed on the basis of in vitro kinetic measurements. The data, assembled into a mathematical model, reproduce in vivo measurements and also provide non‐intuitive predictions. A crucial result is the identification of allosteric interactions whose function is not to couple demand and supply but to maintain a high independence between fluxes in competing pathways. In addition, the model shows that enzyme isoforms are not functionally redundant, because they contribute unequally to the flux and its regulation. Another result is the identification of the threonine concentration as the most sensitive variable in the system, suggesting a regulatory role for threonine at a higher level of integration.     

基于ARIMA模型的生态足迹动态模拟和预测——以甘肃省为例

生态足迹(EF)是一种定量测量人类对自然利用程度的方法。然而目前对其发展趋势准确的定量分析尚不多见。可采用自回归综合移动平均模型(ARIMA)来模拟并预测区域生态足迹。综合运用生态足迹方法和ARIMA模型对甘肃省1949-2009年的生态足迹和生态承载力进行了动态模拟和分析,在此基础上预测了2010-2015年的生态足迹变化趋势。结果表明:1949-2009年,人均生态足迹呈现上升趋势,预计2010-2015年上升趋势明显加快,2015年会增加到2.6051 hm²/人,是2009年的1.67倍;1997-2004年人均生态承载力逐年减少,2005年之后逐年增加,预计2010-2015年仍会增加;预计2010-2015年所有人均生态足迹组成类型均呈现上升趋势,尤以人均化石能源生态足迹增长显著;1997-2009年人均生态承载力均小于人均生态足迹,导致生态赤字,甘肃省生态环境处于不可持续状态,预计2010-2015年人均生态承载力略有增长,但仍小于人均生态足迹,生态赤字不断增大,预计2015年增长到-2.0468 hm²/人,约为2009年(-1.0262 hm²/人)的两倍,甘肃省生态环境不断恶化;经济的发展依赖于化石能源的消耗而造成对自然资源的过度利用,大量耕地转换为建设用地,草地荒漠化是引起甘肃省生态赤字的主要原因;改变经济发展和资源消费模式,控制人口规模,减少人均生态足迹消耗,优化配置和集约节约利用自然资源,提高生态承载力是促进社会经济和资源环境可持续发展的有效途经。     

A stochastic simulation study on using different models for prediction of breeding values while changing the breeding goal

In a stochastic simulation study the effect of simultaneously changing the model for prediction of breeding values and changing the breeding goal was studied. A population of 100 000 cows with registrations on seven traits was simulated in two steps. In the first step of 15 years the population was selected for production and mastitis occurrence using a univariate model for prediction of breeding values for production and a trivariate model using information on mastitis treatments, udder depth and somatic cell score for prediction of breeding values for mastitis occurrence. In the second step six different scenarios were set up and simulated for 15 years combining two different breeding goals and three different models for prediction of breeding values in 20 replicates. Breeding goal 1 had relative economic value per genetic standard deviation on production (19.4) and mastitis occurrence ( − 50) whereas breeding goal 2 had a economic value on production (19.4), udder depth (4.2), mastitis occurrence ( − 50), non return rate (13.0) and days open ( − 16.75). Model 1 was a model similar to the one used in the first 15 years. Model 2 was an approximate multitrait model where solutions for fixed effects from a model corresponding to model 1 were subtracted from the phenotypes and a multitrait model with an overall mean, a year effect, an additive genetic and a residual effect were applied. Model 3 was a full multitrait model. Average genetic trends for total merit and each individual trait over 20 replicates were compared for each scenario. With the number of replicates the genetic responses using model 2 and 3 were not significant different. With a broad breeding goal using, model 2 or model 3 gave a significantly higher response in total merit than using model 1. Using a narrow breeding goal there was no significant difference between models used for prediction of breeding values. Results showed that with a breeding goal with a lot of emphasis on low heritable traits with a high economic value using a multitrait methodology for prediction of breeding values will redistribute the genetic progress in the total merit index. More gain will come from the low heritable traits in the breeding goal and less from traits with higher heritability. With a broad breeding goal and exploiting the available information in the data the inbreeding coefficient increased though not significantly.     

Construction of an intermediate-resolution lattice model and re-examination of the helix-coil transition: a dynamic Monte Carlo simulation

In protein modeling, spatial resolution and computational efficiency are always incompatible. As a compromise, an intermediate-resolution lattice model has been constructed in the present work. Each residue is decomposed into four basic units, i.e. the α-carbon group, the carboxyl group, the imino group, and the side-chain group, and each basic coarse-grained unit is represented by a minimum cubic box with eight lattice sites. The spacing of the lattice is about 0.56?Å, holding the highest spatial resolution for the present lattice protein models. As the first report of this new model, the helix-coil transition of a polyalanine chain was examined via dynamic Monte Carlo simulation. The period of formed α-helix was about 3.68 residues, close to that of a natural α-helix. The resultant backbone motion was found to be in the realistic regions of the conformational space in the Ramachandran plot. Helix propagation constant and nucleation constant were further determined through the dynamic hydrogen bonding process and torsional angle variation, and the results were used to make comparison between classical Zimm-Bragg theory and Lifson-Roig theory based on the Qian-Schellman relationship. The simulation results confirmed that our lattice model can reproduce the helix-coil transition of polypeptide and construct a moderately fine α-helix conformation without significantly weakening the priority in efficiency for a lattice model.     

The importance of root gravitropism for inter-root competition and phosphorus acquisition efficiency: results from a geometric simulation model

We have observed that low soil phosphorus availability alters the gravitropic response of basal roots in common bean (Phaseolus vulgaris L.), resulting in a shallower root system. In this study we use a geometric model to test the hypotheses that a shallower root system is a positive adaptive response to low soil P availability by (1) concentrating root foraging in surface soil horizons, which generally have the highest P availability, and (2) reducing spatial competition for P among roots of the same plant. The growth of nine root systems contrasting in gravitropic response over 320 h was simulated in SimRoot, a dynamic three-dimensional geometric model of root growth and architecture. Phosphorus acquisition and inter-root competition were estimated with Depzone, a program that dynamically models nutrient diffusion to roots. Shallower root systems had greater P acquisition per unit carbon cost than deeper root systems, especially in older root systems. This was due to greater inter-root competition in deeper root systems, as measured by the volume of overlapping P depletion zones. Inter-root competition for P was a significant fraction of total soil P depletion, and increased with increasing values of the P diffusion coefficient (De), with root age, and with increasing root gravitropism. In heterogenous soil having greater P availability in surface horizons, shallower root systems had greater P acquisition than deeper root systems, because of less inter-root competition as well as increased root foraging in the topsoil. Root P acquisition predicted by SimRoot was validated against values for bean P uptake in the field, with an r ² between observed and predicted values of 0.75. Our results support the hypothesis that altered gravitropic sensitivity in P-stressed roots, resulting in a shallower root system, is a positive adaptive response to low P availability by reducing inter-root competition within the same plant and by concentrating root activity in soil domains with the greatest P availability. This revised version was published online in August 2006 with corrections to the Cover Date.