Coupling of an Individual-Based Model of Anchovy with Lower Trophic Level and Hydrodynamic Models

Anchovy （Engraulis aponicus）, a small pelagic fish and food of other economic fishes, is a key species in the Yellow Sea ecosystem. Understanding the mechanisms of its recruitment and biomass variation is important for the prediction and management of fishery resources. Coupled with a hydrodynamic model （POM） and a lower trophic level ecosystem model （NEMURO）, an individual-based model of anchovy is developed to study the influence of physical environment on anchovy＇s biomass variation, Seasonal variations of circulation, water temperature and mix-layer depth from POM are used as external forcing for NEMURO and the anchovy model. Biomasses of large zooplankton and predatory zooplankton which anchovy feeds on are output from NEMURO and are controlled by the consumption of anchovy on them. Survival fitness theory related to temperature and food is used to determine the swimming action of anchovy in the model. The simulation results agree well with observations and elucidate the influence of temperature in over-wintering migration and food in feeding migration.

Simulation Study on the Interannual Variation of the Transport and Distribution of Chub Mackerel (Scomber japonicus) Larvae and Juveniles Using Individual-Based Model

An individual-based model of Scomber japonicus in the East China Sea(ECS)was developed to simulate the effects of physical environment on the transport and distribution of eggs,larvae and juveniles of S.japonicus from 1978 to 2013.The results showed that there were interannual differences in the transport and distribution of eggs,larvae and juveniles of S.japonicus in the ECS due to different physical environments from 1978 to 2013,and this difference was extremely obvious in some specific years.The current in the drift path of eggs and juveniles controlled and affected the transport process and distribution characteristics.In April,the distribution of eggs and larvae was mainly controlled by the Taiwan Warm Current(TWC).The number of eggs and larvae transported into the northeastern waters of the ECS was positively correlated with the intensity of TWC.In May,it was mainly regu-lated by the TWC and the Tsushima Strait Warm Current(TSWC).In June,the number of larvae and juveniles entering the Tsushima Strait and the Pacific Ocean was determined by the TSWC.In general,in the years with high number of larvae and juveniles into the Tsushima Strait,the catch of 0-year-old S.japonicus was also higher.In addition,the number of larvae and juveniles entering the Tsushima Strait in El Niño years was less than that in La Niña years.In July,the transport was mainly controlled by the Kuroshio Current(KC),and the eddy within the KC strongly affected its distribution.

An Individual-Based Modeling Approach to Investigate Sympatric Speciation via Specialized Resource Usage

An individual-based model, EcoSim, was employed to investigate if specialized resource use could promote sympatric speciation. Prey individuals in the original version of EcoSim were supplied with a single primary food resource. A dual resource version with different food resources (Food 1 and Food 2) was also developed to create favorable conditions for the emergence of specialized food consumption among prey individuals. The single resource version was used as the control to determine the impact of the presence of multiple food resources on the occurrence of sympatric speciation. Each unit of Food 2 contained a higher amount of energy than Food 1, and Food 1 was more accessible than Food 2. Initially, prey individuals mostly fed on Food 1. How-ever, after the emergence of food specialization, the consumption rate of Food 2 signifi-cantly exceeded the consumption rate of Food 1;although prey individuals more frequently encountered Food 1. While sympatric speciation was observed in the dual resource version runs, we could not identify any sympatric species in the single resource version runs. Machine learning techniques were also employed to identify the most influential initial conditions leading to sympatric speciation. According to the obtained results, in most lineages sympatric speciation occurred at the beginning of the food specialization pro-cess. When the lineage had a high special diversity, the lineage needed two different criteria to diverge sympatrically: possessing high genetic diversity and a large population size. In support of previous findings, this study demonstrated that the most accurate determination of initial conditions leading to sympatric speciation can be obtained from lineages that are at the beginning of the divergence process. In conclusion, this study indicated that divergent foraging behavior could potentially lead to the sympatric emergence of new species in the absence of geographic isolation.

Effectiveness of non-pharmaceutical interventions against local transmission of COVID-19: An individual-based modelling study

The outbreak of the novel coronavirus disease 2019(COVID-19),caused by the novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),has caused global transmission,and been spread all over the world.For those regions that are currently free of infected cases,it is an urgent issue to prevent and control the local outbreak of COVID-19 when there are sporadic cases.To evaluate the effects of non-pharmaceutical interventions against local transmission of COVID-19,and to forecast the epidemic dynamics after local outbreak of diseases under different control measures,we developed an individual-based model(IBM)to simulate the transmission dynamics of COVID-19 from a microscopic perspective of individual-to-individual contacts to heterogenous among individuals.Based on the model,we simulated the effects of different levels of non-pharmaceutical interventions in controlling disease transmission after the appearance of sporadic cases.Simulations shown that isolation of infected cases and quarantine of close contacts alone would not eliminate the local transmission of COVID-19,and there is a risk of a second wave epidemics.Quarantine the second-layer close contacts can obviously reduce the size of outbreak.Moreover,to effectively eliminate the daily new infections in a short time,it is necessary to reduce the individual-to-individual contacts.IBM provides a numerical representation for the local transmission of infectious diseases,and extends the compartmental models to include individual heterogeneity and the close contacts network.Our study suggests that combinations of self-isolation,quarantine of close contacts,and social distancing would be necessary to block the local transmission of COVID-19.

An individual-based probabilistic model for simulating fisheries population dynamics

The purpose of stock assessment is to support managers to provide intelligent decisions regarding removal from fish populations.Errors in assessment models may have devastating impacts on the population fitness and negative impacts on the economy of the resource users.Thus,accuracte estimations of population size,growth rates are critical for success.Evaluating and testing the behavior and performance of stock assessment models and assessing the consequences of model mis-specification and the impact of management strategies requires an operating model that accurately describe the dynamics of the target species,and can resolve spatial and seasonal changes.In addition,the most thorough evaluations of assessment models use an operating model that takes a different form than the assessment model.This paper presents an individual-based probabilistic model used to simulate the complex dynamics of populations and their associated fisheries.Various components of population dynamics are expressed as random Bernoulli trials in the model and detailed life and fishery histories of each individual are tracked over their life span.The simulation model is designed to be flexible so it can be used for different species and fisheries.It can simulate mixing among multiple stocks and link stock-recruit relationships to environmental factors.Furthermore,the model allows for flexibility in sub-models(e.g.,growth and recruitment)and model assumptions(e.g.,age-or size-dependent selectivity).This model enables the user to conduct various simulation studies,including testing the performance of assessment models under different assumptions,assessing the impacts of model mis-specification and evaluating management strategies.

The impact of salps(Salpa thompsoni)on the Antarctic krill population(Euphausia superba):an individual-based modelling study

Background Krill(Euphausia superba)and salps(Salpa thompsoni)are key macrozooplankton grazers in the Southern Ocean ecosystem.However,due to differing habitat requirements,both species previously exhibited little spatial overlap.With ongoing climate change-induced seawater temperature increase and regional sea ice loss,salps can now extend their spatial distribution into historically krill-dominated areas and increase rapidly due to asexual reproduction when environmental conditions are favorable.Understanding the potential effects on krill is crucial,since krill is a species of exceptional trophic significance in the Southern Ocean food web.Negative impacts on krill could trigger cascading effects on its predators and prey.To address this question,we combined two individual-based models on salps and krill,which describe the whole life cycle of salp individuals and the dynamic energy budget of individual krill.The resulting new model PEKRIS(PErformance of KRIll vs.Salps)simulates a krill population for 100 years under varying chlorophyll-a concentrations in the presence or absence of salps.Results All of the investigated krill population properties(abundance,mean length,and yearly egg production)were significantly impacted by the presence of salps.On the other hand,salp density was not impacted if krill were present.The medians of krill population properties deviated during variable maximum chlorophyll-a density per year when salps were introduced by−99.9%(−234 individuals per 1000 m3)for krill density,−100%(−22,062 eggs per 1000 m3)for krill eggs and−0.9%(−0.3 mm)for mean length of krill.Conclusions If both species compete for the same food resource in a closed space,salps seem to inhibit krill populations.Further simulation studies should investigate whether this effect prevails if different phytoplankton sizes and consumption preferences of krill are implemented.Furthermore,direct predation of the two species or consumption of krill fecal pellets by salps could change the impact size of the food competition.

Assessment of immunization procedures for foot-and-mouth disease in large-scale pig farms in China based on actual data and dynamics

Foot-and-mouth disease(FMD)is an acute,highly infectious and pathogenic animal disease.In recent years,with the rapid development of the swine breeding industry in China,pig farms have shown a trend of larger-scale development.Large-scale pig farms employ standardized management,a high level of automation,and a strict_system.However,these farms have a large trading volume,and increased transmission intensity of FMD is noted inside the farm.At present,the main control measure against FMD is pig vaccination.However,a standard for immunization procedures is not available,and currently adopted immunization procedures have not been effectively and systematically evaluated.Taking a typical large-scale pig farm in China as the research subject and considering the breeding pattern,piggery structure,age structure and immunization procedures,an individual-based state probability model is established to evaluate the effectiveness of the immune procedure.Based on numerical simulation,it is concluded that the optimal immunization program involves primary immunization at 40 days of age and secondary immunization at 80 days of age for commercial pigs.Breeding boars and breeding sows are immunized 4 times a year,and reserve pigs are immunized at 169 and 259 days of age.According to the theoretical analysis,the average control reproduction number of individuals under the optimal immunization procedure in the farm is 0.4927.In the absence of immunization,the average is 1.7498,indicating that the epidemic cannot be controlled without immunization procedures.

Gap models across micro-to mega-scales of time and space:examples of Tansley’s ecosystem concept

Background:Gap models are individual-based models for forests.They simulate dynamic multispecies assemblages over multiple tree-generations and predict forest responses to altered environmental conditions.Their development emphases designation of the significant biological and ecological processes at appropriate time/space scales.Conceptually,they are with consistent with A.G.Tansley’s original definition of"the ecosystem".Results:An example microscale application inspects feedbacks among terrestrial vegetation change,air-quality changes from the vegetation’s release of volatile organic compounds(VOC),and climate change effects on ecosystem production of VOC’s.Gap models can allocate canopy photosynthate to the individual trees whose leaves form the vertical leaf-area profiles.VOC release depends strongly on leaf physiology by species of these trees.Leaf-level VOC emissions increase with climate-warming.Species composition change lowers the abundance of VOC-emitting taxa.In interactions among ecosystem functions and biosphere/atmosphere exchanges,community composition responses can outweigh physiological responses.This contradicts previous studies that emphasize the warming-induced impacts on leaf function.As a mesoscale example,the changes in climate(warming)on forests including pest-insect dynamics demonstrates changes on the both the tree and the insect populations.This is but one of many cases that involve using a gap model to simulate changes in spatial units typical of sampling plots and scaling these to landscape and regional levels.As this is the typical application scale for gap models,other examples are identified.The insect/climatechange can be scaled to regional consequences by simulating survey plots across a continental or subcontinental zone.Forest inventories at these scales are often conducted using independent survey plots distributed across a region.Model construction that mimics this sample design avoids the difficulties in modelling spatial interactions,but we also discuss simulation at these scales with contagion effects.Conclusions:At the global-scale,successful simulations to date have used functional types of plants,rather than tree species.In a final application,the fine-scale predictions of a gap model are compared with data from micrometeorological eddy-covariance towers and then scaled-up to produce maps of global patterns of evapotranspiration,net primary production,gross primary production and respiration.New active-remote-sensing instruments provide opportunities to test these global predictions.

Simulation of the distribution,growth,and survival rate of chub mackerel larvae and juveniles in the East China Sea

In the East China Sea(ECS),chub mackerel Scomber japonicus constitutes an important coastal-pelagic fishery resource that is mainly exploited by Chinese,Japanese,and Korean light-purse seine fisheries.Because the early life history of chub mackerel plays a significant role in its recruitment,we developed an individual-based model to study the distribution,growth,and survival rate of chub mackerel larvae and juveniles in the ECS to improve our understanding of the chub mackerel population structure and recruitment.Our results show that as body length rapidly increases,the swimming capacity of chub mackerel larvae and juveniles improves quickly,and their spatial distribution depends more on their habitat conditions than the ocean currents.Correspondingly,the juveniles from the central and southern ECS spawning ground are scarcely recruited into the Japan/East Sea(JES)or the western Pacific Ocean,but a significant proportion of juveniles from the northern ECS spawning ground still enter the JES and there are exchanges between the stocks in the ECS and JES.Thus,it seems more reasonable to assess and manage the chub mackerels in the ECS and JES as a stock.The water temperature and ocean primary production in the ECS are two important factors influencing the chub mackerel habitat conditions and their spatial and temporal distribution are significantly different as the spawning time changes.Therefore,the spawning time and location play an important role in the growth and survival rate of the larvae and juveniles.Generally,when chub mackerel spawns at the southern ECS spawning ground in March,the larva and juvenile growth and survival rate is relatively high;as spawning time moves forward,higher growth and survival rates would be expected for the chub mackerel spawned coastward or northward.For specific spawning sites,early or delayed spawning will reduce the survival rate.

Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq

Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations;however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.

Mobile population dynamics and malaria vulnerability:a modelling study in the China-Myanmar border region of Yunnan Province,China

Background:The China-Myanmar border region presents a great challenge in malaria elimination in China,and it is essential to understand the relationship between malaria vulnerability and population mobility in this region.Methods:A community-based,cross-sectional survey was performed in five villages of Yingjiang county during September 2016.Finger-prick blood samples were obtained to identify asymptomatic infections,and imported cases were identified in each village(between January 2013 and September 2016).A stochastic simulation model(SSM)was used to test the relationship between population mobility and malaria vulnerability,according to the mechanisms of malaria importation.Results:Thirty-two imported cases were identified in the five villages,with a 4-year average of 1 case/year(range:0-5 cases/year).No parasites were detected in the 353 blood samples from 2016.The median density of malaria vulnerability was 0.012(range:0.000-0.033).The average proportion of mobile members of the study population was 32.56%(range:28.38-71.95%).Most mobile individuals lived indoors at night with mosquito protection.The SSM model fit the investigated data(χ2=0.487,P=0.485).The average probability of infection in the members of the population that moved to Myanmar was 0.011(range:0.0048-0.1585).The values for simulated vulnerability increased with greater population mobility in each village.Conclusions:A high proportion of population mobility was associated with greater malaria vulnerability in the China-Myanmar border region.Mobile population-specific measures should be used to decrease the risk of malaria re-establishment in China.

Social networks improve leaderless group navigation by facilitating long-distance communication

Group navigation is of great importance for many animals, such as migrating flocks of birds or shoals of fish. One theory states that group membership can improve navigational accuracy compared to limited or less accurate individual naviga- tional ability in groups without leaders （＂Many-wrongs principle＂）. Here, we simulate leaderless group navigation that includes social connections as preferential interactions between individuals. Our results suggest that underlying social networks can reduce navigational errors of groups and increase group cohesion. We use network summary statistics, in particular network motifs, to study which characteristics of networks lead to these improvements. It is networks in which preferences between individuals are not clustered, but spread evenly across the group that are advantageous in group navigation by effectively enhancing long-distance information exchange within groups. We suggest that our work predicts a base-line for the type of social structure we might expect to find in group-living animals that navigate without leaders

Relationship between the Virtual Dynamic Thinning Line and the Self-Thinning Boundary Line in Simulated Plant Populations

The self-thinning rule defines a straight upper boundary line on log-log scales for all possible combinations of mean individual biomass and density in plant populations. Recently, the traditional slope of the upper boundary line, -3/2, has been challenged by -4/3 which is deduced from some new mechanical theories, like the metabolic theory. More experimental or field studies should be carried out to identify the more accurate self-thinning exponent. But it＇s hard to obtain the accurate self-thinning exponent by fitting to data points directly because of the intrinsic problem of subjectivity in data selection. The virtual dynamic thinning line is derived from the competition-density （C-D） effect as the initial density tends to be positive infinity, avoiding the data selection process. The purpose of this study was to study the relationship between the virtual dynamic thinning line and the upper boundary line in simulated plant stands. Our research showed that the upper boundary line and the virtual dynamic thinning line were both straight lines on log-log scales. The slopes were almost the same value with only a very little difference of 0.059, and the intercept of the upper boundary line was a little larger than that of the virtual dynamic thinning line. As initial size and spatial distribution patterns became more uniform, the virtual dynamic thinning line was more similar to the upper boundary line. This implies that, given appropriate parameters, the virtual dynamic thinning line may be used as the upper boundary line in simulated plant stands.

Modelling COVID-19 epidemic with confirmed cases-driven contact tracing quarantine

The pandemic of novel coronavirus disease 2019(COVID-19)has been a severe threat to public health.The policy of close contract tracing quarantine is an effective strategy in controlling the COVID-19 epidemic outbreak.In this paper,we developed a mathematical model of the COVID-19 epidemic with confirmed case-driven contact tracing quarantine,and applied the model to evaluate the effectiveness of the policy of contact tracing and quarantine.The model is established based on the combination of the compartmental model and individual-based model simulations,which results in a closed-form delay differential equation model.The proposed model includes a novel form of quarantine functions to represent the number of quarantine individuals following the confirmed cases every day and provides analytic expressions to study the effects of changing the quarantine rate.The proposed model can be applied to epidemic dynamics during the period of community spread and when the policy of confirmed cases-driven contact tracing quarantine is efficient.We applied the model to study the effectiveness of contact tracing and quarantine.The proposed delay differential equation model can describe the average epidemic dynamics of the stochastic-individual-based model,however,it is not enough to describe the diverse response due to the stochastic effect.Based on model simulations,we found that the policy of contact tracing and quarantine can obviously reduce the epidemic size,however,may not be enough to achieve zero-infectious in a short time,a combination of close contact quarantine and social contact restriction is required to achieve zeroinfectious.Moreover,the effect of reducing epidemic size is insensitive to the period of quarantine,there are no significant changes in the epidemic dynamics when the quarantine days vary from 7 to 21 days.

Stochastic rules for predator and prey hunting and escape behavior in a lattice-based model

Understanding of ecosystem resilience and stability requires comprehending predator- prey dynamics because ecosystems consist of dynamically interacting subsystems that include predator-prey relationships. This relationship is closely related to the hunting- escaping strategies employed by the predator and prey. Therefore, understanding the effects of hunting and escaping strategies on ecosystems will lead to a better under- standing of these systems. As an approach for describing the predator-prey interaction, lattice-based models have been adopted because this approach has strong advantages for simulating various dynamical processes of individual-individual interaction. In the models, each lattice cell is either considered as an attractive/repulsive cell, or an indi- vidual cell, or else it is empty. The attractive （or repulsive cell） can be interpreted as the prey （or predator） of the individual. These states allow us to incorporate the ecological processes of local antagonistic interactions, namely the spread of disturbances （by the predator） and regrowth or recovery （by the prey）. These processes are directly related to the strategic behavior of individuals, such as hunting and escaping. In this study, we suggest a simple and effective mapping formula as a stochastic rule to describe the hunt- ing and escaping behavior. This formula could be widely used not only in the behavior but also in competitive and cooperative relationships.