Phylogeography,genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences:A systematic review and meta-analysis

Objective: To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country.Methods: We searched electronic databases including Medline, Pub Med, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran.Results: T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5(Acanthamoeba lenticulata), T6, T9, T11, T13 and T15(Acanthamoeba jacobsi).A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6(34.1%) and IR7(31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity(0.612–0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18 S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index(FST) was from low to high values(0.024 33–0.418 92). The statistically FST points out that T4 is genetically differentiated between north-west, north-south and centralsouth metapopulations, but not differentiated between west-central, west-south, centralsouth, and north-central isolates.Conclusions: An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals/sources among the various regions of Iran.

Metapopulation的概念及其在植物种群生态学中的应用（I）Metapopulation概念的理解和辨析

Ｍｅｔａｐｏｐｕｌａｔｉｏｎ的概念及其在植物种群生态学中的应用（Ｉ）Ｍｅｔａｐｏｐｕｌａｔｉｏｎ概念的理解和辨析叶万辉关文彬（黑龙江中医学院哈尔滨１５００４０）（东北林业大学哈尔滨１５００４０）刘正恩（黑龙江中医学院哈尔滨１５００４０）Ｃｏｎｃｅｐｔ...

Metapopulation(复合种群 )究竟是什么 ?

Metapopulation是种群生态学、景观生态学和保护生物学诸领域中的一个重要概念。近年来 ,有关metapulation的中文文章频繁地出现在生态学杂志和书籍中。这一现象很好地反映了国内外华人生态学者对有关metapopulation的问题愈来愈感兴趣 ,但对同一英文词出现的多种中文译法不免给读者造成了一些概念上的混乱 ,同时似乎也反映了作者们对 metapopulation这一概念在理解上的差异。因此 ,本文拟对 metapopulation及其有关概念的涵义和发展加以讨论 ,并对现有的几种译文的确切性作一分析 ,以与生态学同行商榷。

具年龄结构的metapopulation的空间分布模型

运用Leslie矩阵和Markov链建立了一个具年龄结构的集合种群随时间动态变化的空间分布模型,给出了集 合种群持续存在以及灭绝的条件.

Stochastic resonance for a metapopulation system driven by multiplicative and additive colored noises

We investigate the stochastic resonance （SR） phenomenon induced by the periodic signal in a metapopulation system with colored noises. The analytical expression of signal-to-noise is derived in the adiabatic limit. By numerical calculation, the effects of the addictive noise intensity, the multiplicative noise intensity and two noise self-correlation times on SNR are respectively discussed. It shows that： （i） in the case that the addictive noise intensity M takes a small value, a SR phenomenon for the curve of SNR appears; however, when M takes a large value, SNR turns into a monotonic function on the multiplicative noise intensity Q. （ii） The resonance peaks in the plots of the multiplicative noise intensity Q versus its self-correlation time Vl and the addictive noise intensity M versus its self-correlation time ~2 translate in parallel. Mean- while, a parallel translation also appears in the plots of vl versus Q and v2 versus M. （iii） The interactive effects between self-correlation times Vl and v2 are opposite.

Spatial and temporal distribution of the gastropod Heleobia australis in an eutrophic estuarine system suggests a metapopulation dynamics

Hydrobiidae is one of the most diverse taxa among limnic and estuarine mollusks. Patterns of spatial and seasonal distribution of Heleobia australis were studied in ten stations over two years, in the urban eutrophic bay of Guanabara, Rio de Janeiro, Brazil. Spatial dispersal strategies in adults of this species, analyzed in the laboratory, revealed three patterns: 1) mobility on soft sediments;2) mobility on hard substrata;and 3) the ability to lift from the bottom to the surface, to again sink down. This facilitate species movement from one location to another by surface currents or attached to floating debris. Thus, individuals are able to escape from an impacted area and further re-colonize other patches after recovering from local impacts. The hypothesis of metapopulation dynamics (source– sink) was analyzed. Two stations with high and constant numbers of individuals were grouped and tested as possible ‘sources’. The number of specimens in the remaining stations was highly variable, even with the complete disappearance and posterior highly dense re-occurrence of the mollusk, whereby these were tested as possible ‘sinks’. Results derived from nested ANOVA supported the hypothesis of metapopulation dynamics in the case of H. australis adults, ex-pressed through opportunistic-species domi- nation of a highly impacted estuarine system, such as Guanabara Bay.

Dynamics and Control of Infectious Diseases in Stochastic Metapopulation Models

The research on spatial epidemic models is a topic of considerable recent interest. In another hand, the advances in computer technology have stimulated the development of stochastic models. Metapopulation models are spatial designs that involve movements of individuals between distinct subpopulations. The purpose of the present work has been to develop stochastic models in order to study the transmission dynamics and control of infectious diseases in metapopulations. The authors studied Susceptible-Infected-Susceptible （SIS） and Susceptible-lnfected-Recovered （SIR） epidemic schemes, using the Gillespie algorithm, Computational numerical simulations were carried in order to explore the models. The results obtained show how the dynamics of transmission and the application of control measures within each subpopulation may affect all subpopulations of the system. They also show how the distribution of control measures among subpopulations affects the efficacy of these strategies. The dynamics of the stochastic models developed in the current study follow the trends observed in the classic deterministic designs. Also, the present models exhibit fluctuating behavior. This work highlights the importance of the spatial distribution of the population in spread and control of infectious diseases. In addition, it shows how chance could play an important role in these scenarios.

Extinction Time of a Metapopulation Driven by Colored Correlated Noises

The simplified incidence function model which is driven by the colored correlated noises is employed to investigate the extinction time of a metapopulation perturbed by environments. The approximate Fokker-Planck Equation and the mean first passage time which denotes the extinction time （Tex） are obtained by virtue of the Novikov theorem and the Fox approach. After introducing a noise intensity ratio and a dimensionless parameter R = D /α （D and a are the multiplicative and additive colored noise intensities respectively）, and then performing numerical computations, the results indicate that： （i） The absolute value of correlation strength A and its correlation time τ3 play opposite roles on the Tex; （ii） For the case of 0 〈λ〈 1,α and its correlation time τ2 play opposite roles on the Tex in which R〉 1 is the best condition, and there is one-peak structure on the Tex - D plot; （iii） For the case of-1 〈 λ≤ 0, D and its correlation time τ1 play opposite roles on the Tex in which R 〈 1 is the best condition and there is one-peak structure on the Tex - τ2 plot.

High philopatry rates of Yellow-legged Gulls in the southeastern part of the Bay of Biscay

Background:Philopatry rate is one of the main factors shaping population dynamics in colonial seabirds.Low rates of philopatry are linked to populations with high dispersal,while high rates are linked to populations with a very high spatial structure pattern(i.e.,metapopulations).The Cantabrian Yellow-legged Gull(Larus michahellis)population is considered to be resident,with relatively low dispersal rates.Precise estimations of its philopatry rates are however still lacking.Here,we aimed to estimate philopatry rates in the main Yellow-legged Gull colonies of the province of Gipuzkoa,in the southeastern part of the Bay of Biscay.Methods:We analysed 734 resightings,during the breeding season at the colonies of Getaria,Santa Clara and Ulia,relative to a total of 3245 individuals ringed at birth in these same colonies during a period of 13 years.These data were analysed using Multi-State Recapture models in MARK.Results:After controlling survival and resighting probability,the average dispersal rate among colonies was 4%(±SD=2%)when individuals are immature,decreasing to 1±1%)for adult breeding gulls(i.e.,philopatry rate was 99%).Annual survival rates were assessed to be 0.27±0.02 for birds in their first year of life and 0.87±0.01 for older individuals.The probability of observing immature birds in the colonies was 0.08±0.01,as compared to 0.21±0.02 in adult birds.Conclusions:We obtained evidence of extremely high local philopatry rates,clearly within the upper limit found in gulls.A high philopatry favour a speciation in these species who are vulnerable to obtain the main food source(land-fills and fishing discard)which are transforming under new ecological process.

Research Progress on the Theory of Delineation and Zoning of Nature Reserves in China and Discussion of Strategies

The construction of nature reserves plays an essential role in protecting natural resources and the ecological environment,especially the conservation of rare and endangered species,which also has a vital function in maintaining the ecological security of the national territory.China has built up a comprehensive network of nature reserves after waves of development,but there are still many problems with the management of nature reserves,such as the definition of boundaries,zoning theory,zoning methods,and legal protection.The definition of boundaries is a tool for effective management of nature reserves,but achieving scientific and effective boundary definition is a difficult problem for the construction and management of reserves.It is also a problem that must be solved to achieve sustainable development.This paper compared three fundamental theories of the conservation of species in nature reserves,namely island biogeography,metapopulation,and landscape ecology,from connotations,applications and advantages,and disadvantages,and discussed the progress of theoretical research to provide valuable references for the definition and planning of effective boundaries of nature reserves.

Does landscape structure contribute to the long-term maintenance of generalized parasitism in cowbirds?

Unlike most brood parasites, several species of cowbird (Molothrus) are generalists that parasitize multiple host species across their range and within the same communities; likewise, there is little evidence that individuals within a population specialize on host species. This situation has variously been attributed to the recency of cowbird evolution (the 'evolutionary lag' hypothesis) or to hidden costs of rejection by hosts (the 'equilibrium' hypothesis). Both hypotheses have some support as cowbirds are indeed a relatively young clade compared with more specialized cuckoos and cowbirds are capable of sophisticated behaviors such as retaliation against rejection ('mafia' behaviors) that would select for acceptance of cowbird eggs. Nevertheless, many species in the Americas have evolved specialized defenses against cowbird parasitism, almost all of which live in more open habitats (e. g., grasslands, shrublands, riparian strips), which indicates that coevolutionary processes can operate in ways that select for host defenses in spite of cowbird counterdefenses. We propose that the structure of landscapes in North America may explain why forest-nesting birds lack defenses against parasitism and reinforce the long-term maintenance of generalized brood parasitism in cowbirds. Because cowbirds require open habitats in which to feed, they are rare or absent in large forest tracts, which dominate much of the forest cover of the Americas. These tracts act as 'source habitats' that produce surplus young that recolonize populations in smaller, fragmented forest patches in which rates of both cowbird parasitism and nest predation are very high ('sink' habitats). Evolution of antiparasite adaptations would be very slow in this situation because most hosts are produced in areas where there is little or no cowbird parasitism. In addition, the interplay of host breeding dispersal, source-sink metapopulation dynamics, and fragmented forest habitat could further deter the evolution of host defenses against parasitism. Therefore, as long as large forest tracts remain widespread in North America, most forest birds will likely continue to lack defenses against cowbird parasitism, guaranteeing a steady supply of na ve hosts in forest habitats, even in fragmented landscapes. This situation will, in turn, favor host generalist cowbirds that actively avoid more open habitats in favor of parasitizing forest bird communities. These forest communities may also act as source populations for cowbirds, which might pump surplus generalist cowbirds into more open habitats further slowing the coevolutionary process. As long as large forest tracts are a common part of the landscape, generalist parasitism may persist indefinitely.

A Metapopulation Model with Patches Distributed in Two Geographical Scales

We propose a metapopulation model with two geographical scales. In a regional scale, the model describes the dynamics of a collection of habitats connected by migratory movements. In a local scale, we consider some granularity within each habitat, in the sense that each habitat is itself a collection of patches linked by dispersal. The whole ensemble can be seen as a metapopulation composed by local metapopulations. We analyze the synchronization of the model in the two geographical scales. We present an analytic criterion for synchronization where only the habitats in the regional scale evolve with the same dynamics. Through numerical simulations, we discuss the different synchronization modes. It depends on how the individuals are distributed in the local patches that compose a habitat after migration takes place in the regional scale.

Recovery Process on Soft-Bottom Macrobenthic Communities after Artificial Disturbance in Tropical Polluted Estuary(Guanabara Bay,Rio de Janeiro,Brazil)

The regime of disturbance with natural or anthropogenic origin can lead to the destabilization or even to a mass mortality of benthic communities. Due to the heterogeneity of the disturbance there is a formation of patches in different stages of ecological succession. The aim of this study is to follow and describe the resilience in artificial disturbed sediment in a polluted bay in Rio de Janeiro. The sediment was collected, sterilized and placed inside corers (10 cmdiameter ×15 cmheight) in the same place where it was collected. We allocated the samples in two structures, the difference between them was that one was placed closed to the bottom and the other was placed50 cmheight. We found 2352 organisms distributed in 14 taxons. The class Polychaeta and the order Amphipoda showed the highest density in all the survey and treatments. We identified the factors influencing the scenarium: different mechanisms of dispersal, the position of the structures and life history of each group. Disturbance can be the main cause of the patch’s diversity found in estuaries and coastal areas. Because of this, monitoring of selected areas becomes an important tool to understand the regime of disturbance as a key factor structuring benthic communities in soft sediment, also suggesting a metapopulation dynamics.

Epidemicity indices and reproduction numbers from infectious disease data in connected human populations

We focus on distinctive data-driven measures of the fate of ongoing epidemics.The relevance of our pursuit is suggested by recent results proving that the short-term temporal evolution of infection spread is described by an epidemicity index related to the maximum instantaneous growth rate of new infections,echoing concepts and tools developed to study the reactivity of ecosystems.Suitable epidemicity indices can showcase the dynamics of infections,together with commonly employed effective reproduction numbers,especially when the latter assume values less than 1.In particular,epidemicity evaluates the short-term reactivity to perturbations of a disease-free equilibrium.Here,we show that sufficient epidemicity thresholds to prevent transient epidemic outbreaks in a spatially connected setting can be estimated by generalizing existing analogues derived when spatial effects are neglected.We specifically account for the discrete nature,in both space and time,of surveillance data of the type typically employed to estimate effective reproduction numbers that formed the bulk of the communication of the state of the COVID-19 pandemic and its controls.After analyzing the effects of spatial heterogeneity on the considered prognostic indicators,we perform a short-and long-term analysis on the COVID-19 pandemic in Italy,showing that endemic conditions were maintained throughout the duration of our simulation despite stringent control measures.Our method provides a portfolio of prognostic indices that are essential to pinpoint the ongoing pandemic in both a qualitative and quantitative manner,as our results demonstrate.We base our conclusions on extended investigations of the effects of spatial fragmentation of communities of different sizes owing to connectivity by human mobility and contact scenarios,within real geographic contexts and synthetic setups designed to test our framework.

A compartment and metapopulation model of Rocky Mountain spotted fever in southwestern United States and northern Mexico

Rocky Mountain spotted fever(RMSF)is a fatal tick-borne zoonotic disease that has emerged as an epidemic in western North America since the turn of the 21st century.Along the US south-western border and across northern Mexico,the brown dog tick,Rhipicephalus sanguineus,is responsible for spreading the disease between dogs and humans.The widespread nature of the disease and the ongoing epidemics contrast with historically sporadic patterns of the disease.Because dogs are amplifying hosts for the Rickettsia rickettsii bacteria,transmission dynamics between dogs and ticks are critical for understanding the epidemic.In this paper,we developed a compartment metapopulation model and used it to explore the dynamics and drivers of RMSF in dogs and brown dog ticks in a theoretical region in western North America.We discovered that there is an extended lag—as much as two years—between introduction of the pathogen to a naïve population and epidemic-level transmission,suggesting that infected ticks could disseminate extensively before disease is detected.A single large city-size population of dogs was sufficient to maintain the disease over a decade and serve as a source for disease in surrounding smaller towns.This model is a novel tool that can be used to identify high risk areas and key intervention points for epidemic RMSF spread by brown dog ticks.

The role of behavior in tern conservation

Behavioral research has long had an important role in the conservation of terns （Ayes： Stemidae）. Habitat management and restoration of breeding colony sites depends on knowledge of the cues used to select colony and nest sites. For example, conspecific attraction with playback and decoys is commonly used to bring terns to suitable colony sites and habitat modification is often used to increase the availability of suitable nest sites. Tern colonies are interconnected by dispersal, and a metapopulation approach is needed for effective management. Population dynamics are therefore affected by behaviors that influence the frequency of movement among colony sites： site fidelity, natal and breeding dispersal, and group adherence. The monogamous breeding system of terns should keep effective population size similar to census population size, but variation in sex ratios （likely resulting from sex differences in behavior） and in parental quality can result in a smaller than expected effective population size. In addition to the behavior of terns, knowledge of the behavior of predators on terns contributes to management plans, because predator behavior can sometimes be manipulated and predation is often performed by only a few specialized individuals. Other examples of links between tern behavior and conservation are also briefly reviewed, such as behavioral toxicology research and studies of behavioral responses to human disturbance and manmade structures. More work is needed on the behavior of migratory terns at staging sites, stopover sites and wintering grounds, and on the behavior of less well-studied species and species in less well-studied geographic regions [Current Zoology 60 （4）： 500-514, 2014].

Dispersing male Parnassius smintheus butterflies are more strongly affected by forest matrix than are females

Dispersal is a central aspect of the ecology, evolution, and conservation of species. Predicting how species will respond to changing environmental conditions requires understanding factors that produce variation in dispersal. We explore one source of variation, differences between sexes within a spatial population network. Here, we compare the dispersal patterns of male and female Parnassius smintheus among 18 subpopulations over 8 years using the Virtual Migration Model. Estimated dispersal parameters differed between males and females, particularly with respect to movement through meadow and forest matrix habitat. The estimated dispersal distances of males through forest were much less than for females. Observations of female movement showed that, unlike males, females do not avoid forest nor does forest exert an edge effect. We explored whether further forest encroachment in this system would have different effects for males and females by fitting mean parameter estimates to the landscape configuration seen in 1993 and 2012. Despite differences in their dispersal due presumably to both habitat and physiological differences, males and females are predicted to respond in similar ways to reduced meadow area and increased forest isolation.

Dynamics of COVID-19 pandemic in India and Pakistan: A metapopulation modelling approach

India has been the latest global epicenter for COVID-19,a novel coronavirus disease that emerged in China in late 2019.We present a base mathematical model for the transmission dynamics of COVID-19 in India and its neighbor,Pakistan.The base model was rigorously analyzed and parameterized using cumulative COVID-19 mortality data from each of the two countries.The model was used to assess the population-level impact of the control and mitigation strategies implemented in the two countries(notably non-pharmaceutical interventions).Numerical simulations of the basic model indicate that,based on the current baseline levels of the control and mitigation strategies implemented,the pandemic trajectory in India is on a downward trend.This downward trend will be reversed,and India will be recording mild outbreaks,if the control and mitigation strategies are relaxed from their current levels.By early September 2021,our simulations suggest that India could record up to 460,000 cumulative deaths under baseline levels of the implemented control strategies,while Pakistan(where the pandemic is comparatively milder)could see over 24,000 cumulative deaths at current mitigation levels.The basic model was extended to assess the impact of back-and-forth mobility between the two countries.Simulations of the resulting metapopulation model show that the burden of the COVID-19 pandemic in Pakistan increases with increasing values of the average time residents of India spend in Pakistan,with daily mortality in Pakistan peaking in mid-August to mid-September of 2021.Under the respective baseline control scenarios,our simulations show that the backand-forth mobility between India and Pakistan could delay the time-to-elimination of the COVID-19 pandemic in India and Pakistan to November 2022 and July 2022,respectively.

Effect of cultivating croplands and grazing in arid grassland habitats on the conservation of melitaeine butterflies in a mountainous area in Northern China

In the study area (Yanjiaping Village, Hebei Province, China), grazing extensity varies at different loca-tions, small and discontinuous croplands are imbedded in some arid grassland, which are habitats for the melitaeine butterflies, Euphydryas aurinia and Melitaea phoebe. These two species of butterflies coexist in this area, in which grazing and cultivation are the main disturbances. Grazing and cultivation have a reciprocal effect on E. aurinia, rather than M. phoebe. We observed that E. aurinia preferred to occupy patches with moderate grazing and imbedded with small and discontinuous croplands, where E. aurinia also has high population density. The percentage of E. aurinia larval groups in the ribbings was significantly higher than that of M. phoebe, whereas larvae of both species tended to increase in recent years. Our data also showed that the population density and the patch occupancy rate of both E. aurinia and M. phoebe were the highest under moderate grazing. It indicates that cultivation of small and dis-continuous croplands within the patch has a significant effect on the population density of both spe-cies of melitaeine butterflies. Thus, to artificially create or maintain semi-natural habitats, comple-mented by moderate grazing, might be an ecological strategy to conserve melitaeine butterflies effec-tively. Considering the distinct impacts of cultivation and grazing on the population distribution and dynamics of the two different species, human disturbance in the mountainous area might be strategi-cally involved in proposing conservation plans for the target species in the future.