Community pattern analysis: A method for quantifying community mosaic structure

A method of quantifying community spatial patterns, community pattern analysis, is described. It is proposed that ordination analysis is used to obtain an integrated score for each quadrat from transect data. For the data presented here, separate ordinations were made of both floristic and environmental (soils) data. The ordination axis scores are then analysed using two or three-term local variance analysis to quantify the scales of community pattern. Correlation analyses allow the relationship between the vegetation and soils data (as represented by ordination axis scores), and other environmental data to be investigated at defined scales. The advantages of this method, that employs the joint application of conventional methods, are that it includes the influence of all species in the analysis, and that multiple uncorrelated scales of pattern within a community are identified.     

Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics

Terminal restriction fragment length polymorphism (T-RFLP) is increasingly being used to examine microbial community structure and accordingly, a range of approaches have been used to analyze data sets. A number of published reports have included data and results that were statistically flawed or lacked rigorous statistical testing. A range of simple, yet powerful techniques are available to examine community data, however their use is seldom, if ever, discussed in microbial literature. We describe an approach that overcomes some of the problems associated with analyzing community datasets and offer an approach that makes data interpretation simple and effective. The Bray-Curtis coefficient is suggested as an ideal coefficient to be used for the construction of similarity matrices. Its strengths include its ability to deal with data sets containing multiple blocks of zeros in a meaningful manner. Non-metric multi-dimensional scaling is described as a powerful, yet easily interpreted method to examine community patterns based on T-RFLP data. Importantly, we describe the use of significance testing of data sets to allow quantitative assessment of similarity, removing subjectivity in comparing complex data sets. Finally, we introduce a quantitative measure of sample dispersion and suggest its usefulness in describing site heterogeneity. This revised version was published online in June 2006 with corrections to the Cover Date.     

Investigating the causes of fish community change in the Dahan River (Taiwan) using an autecology matrix

Recent work in river restoration and water resources management has seen the need to change the focus of analysis from reach to watershed scales to better define causes of watershed impairment. However, comprehensive investigations at a watershed scale are hindered by difficulties in using reach data that was collected for analysis at small spatial and short temporal scales. This is especially true for ecological and biological data. The approach assembles assessment and monitoring data and uses an autecology matrix to identify the changes in environmental and ecological conditions that may be associated with community change over spatial and temporal scales appropriate for ecosystem analysis in watersheds. The analysis uses a weight-of-evidence approach based on the percent of the community associated with a matrix factor. We have used the autecology matrix to examine historical fish community data from the Dahan River, Taiwan. The results show that the method provides an improved understanding of historical influences on fish community structure and supports a process-based analysis of community change over watershed scales and historic time periods. Further the method helps identify habitat requirements for the fish communities at each sampling site, supporting management and ecological restoration objectives.     

Multiple Lattice Model for Influenza Spreading

Behavioral differences among age classes, together with the natural tendency of individuals to prefer contacts with individuals of similar age, naturally point to the existence of a community structure in the population network, in which each community can be identified with a different age class. Data on age-dependent contact patterns also reveal how relevant is the role of the population age structure in shaping the spreading of an infectious disease. In the present paper we propose a simple model for epidemic spreading, in which a contact network with an intrinsic community structure is coupled with a simple stochastic SIR model for the epidemic spreading. The population is divided in 4 different age-communities and hosted on a multiple lattice, each community occupying a specific age-lattice. Individuals are allowed to move freely to nearest neighbor empty sites on the age-lattice. Different communities are connected with each other by means of inter-lattices edges, with a different number of external links connecting different age class populations. The parameters of the contact network model are fixed by requiring the simulated data to fully reproduce the contact patterns matrices of the Polymod survey. The paper shows that adopting a topology which better implements the age-class community structure of the population, one gets a better agreement between experimental contact patterns and simulated data, and this also improves the accordance between simulated and experimental data on the epidemic spreading.     

宜昌百里荒草山草坡群落物种分布的空间趋势分析

通过基于CCA的趋势面分析和空间插值方法,研究了宜昌百里荒山地草场的群落结构空间变化,以及群落结构空间趋势与主要环境因子的相关性。结果表明,该群落物种空间中的群落结构面和物理空间中的空间趋势面可以很好地吻合,说明该群落的结构由一种具有强烈空间结构化特征的机制控制。对群落结构和空间趋势影响最显著的环境因素是土壤有效磷。     

A new integrative framework for large‐scale assessments of biodiversity and community dynamics,using littoral gastropods and crabs of British Columbia,Canada

Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here, we present and apply an integrative approach that links high‐throughput, multicharacter taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community‐level data set. We collected 1195 gastropods and crabs in British Columbia. First, the General mixed Yule‐coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species‐hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co‐occurrence patterns for nonrandomness using community‐wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species‐hypotheses in community‐level data sets. Nonrandom species co‐occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of carnivorous gastropods and crabs appeared influenced by random processes. Species‐pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co‐occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.     

沈阳地区稻田节肢动物群落结构及群落生态研究

通过对沈阳地区稻田生态系统节肢动物群落结构及群落生态研究。共查得。属昆虫纲的有10个目的29科66种,其中天敌昆虫种类有7目20科51种,属蜘蛛纲的有蜘蛛目10科20种。用空间及时间生态位分析了害虫与天敌两个营养阶层间的关系。稻田生态系统节肢动物的多样性指数、均匀度与优势度分析表明,各类群落受外界干扰都很敏感,且表现一致性。依据节肢动物群落的结构及规律,结合沈阳地区水稻生长、栽培条件,用最优分割方法将稻田群落分为4个阶段,并提出了不同阶段害虫群落特点及害虫防治对策。     

OpenUp! Creating a cross-domain pipeline for natural history data

Multimedia data held by Natural History Museums and Universities are presently not readily accessible, even within the natural history community itself. The EU project OpenUp! is an effort to mobilise scientific biological multimedia resources and open them to a wider audience using the EUROPEANA data standards and portal. The connection between natural history and EUROPEANA is accomplished using well established BioCASe and GBIF technologies. This is complemented with a system for data quality control, data transformation and semantic enrichment. With this approach, OpenUp! will provide at least 1,1 Million multimedia objects to EUROPEANA by 2014. Its lean infrastructure is sustainable within the natural history community and will remain functional and effective in the post-project phase.     

Private and public determinants of child nutrition in Nicaragua and Western Honduras

We present a multivariate regression model of nutritional indicators, including interactions between education levels and overall community development, as well as estimates of community fixed effects, for two data sets: the first one is from a 2001 nationwide household survey in Nicaragua while the second set was collected in the Western regions of Honduras in 2002, as part of an evaluation process for a family entitlement program. Maternal stature, age difference with an older sibling, household size and income are seen as the main determinants of anthropometric development. Within the more homogeneous communities of Western Honduras, woman's education is also related to the child's nutritional status. The importance of individual community variables is much lower and the inclusion of community fixed effects does not alter the other parameters. However, in the Honduran sample, overall community development (assessed through the community fixed effects) has a small but significant and synergistic effect on the impact of child and household variables. The characteristics of this study and the complex design of entitlement programs prevent an adequate evaluation of those interventions within the poverty reduction strategies. The improvement of intra-community targeting seems to be a key orientation for redesign. An improved socio-economic situation, sound population and family policies, and an appropriate preventive public health care still are safe investments towards improvement of child health and nutrition.     

应用间接排序识别盐沼植被的光谱特征:以崇明东滩为例

遥感技术已成为大尺度植被分类的重要手段,而地面植物群落特征与其光谱特征之间的关系是解译遥感影像的关键。该研究选择上海崇明东滩自然保护区的盐沼植物群落为对象,应用ASD地物光谱仪测定其植物群落的光谱反射率,并采用10个小型机载成像光谱仪(CASI)默认植被波段组,应用主分量分析法和相关分析分析了不同群落光谱特征与生态环境因子之间的关系。分析结果表明,间接排序法PCA能够识别盐沼植被中光滩、海三棱 草(Scirpus mariqueter)群落、芦苇(Phragmites australis)群落和互花米草(Spartina alterniflora)等群落的光谱特征,绝大多数盐沼湿地植物群落组成与光谱特征之间有显著的相关,识别效果最好的波段组是736~744 nm、746~753 nm、775~784 nm、815~824 nm和860~870 nm;对光谱反射率影响最大的生态环境因子分别是植物群落的高度和盖度,高程和其它环境因子的影响次之。研究成果可为遥感监测崇明东滩自然保护区内入侵种互花米草的空间分布和扩散规律提供技术支撑,为高光谱遥感影像的影像判读和解译分类以及盐沼湿地植被制图提供科学依据。     

Analysis of treatment effects on the microbial ecology of the human intestine

A large number of studies have investigated gastrointestinal microbiota and changes in the gastrointestinal community. However, a concern in these studies is how best to assess changes in gastrointestinal community structure. This paper presents two different human trials where the fecal terminal restriction fragment length polymorphism data sets were analyzed to search for treatment effects. Principle components analysis and cluster analysis based on grouped data are compared with analysis of data by subject using distance coefficients. Comparison with baseline within an individual before grouping by treatment provided a clearer indication of treatment effects than did an evaluation of data grouped before analysis. In addition, a large within-subject sample size and multiple baseline samples are necessary to accurately analyze treatment effects.     

The maize genetics and genomics database. The community resource for access to diverse maize data

The Maize Genetics and Genomics Database (MaizeGDB) serves the maize (Zea mays) research community by making a wealth of genetics and genomics data available through an intuitive Web-based interface. The goals of the MaizeGDB project are 3-fold: to provide a central repository for public maize information; to present the data through the MaizeGDB Web site in a way that recapitulates biological relationships; and to provide an array of computational tools that address biological questions in an easy-to-use manner at the site. In addition to these primary tasks, MaizeGDB team members also serve the community of maize geneticists by lending technical support for community activities, including the annual Maize Genetics Conference and various workshops, teaching researchers to use both the MaizeGDB Web site and Community Curation Tools, and engaging in collaboration with individual research groups to make their unique data types available through MaizeGDB.     

Testing for local species saturation with nonindependent regional species pools

Identifying the factors controlling local community structure is a central problem in ecology. Ecologists frequently use regression to test for a nonlinear saturating relationship between local community richness and regional species pool richness, suggesting that species interactions limit the number of locally coexisting species. However, communities in different regions are not independent if regions share species. We present a Monte Carlo test for whether an observed local-regional richness relationship is significantly different from that expected when regions are nonindependent and species interactions do not limit community membership. We illustrate this test with data from experimental microcosm communities. A conventional F -test suggests a significant saturating relationship between realized community richness and species pool richness. However, the Monte Carlo test fails to reject the null hypothesis that species interactions do not affect community richness. Strong species interactions do not necessarily set an absolute upper limit to the number of locally coexisting species.     

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel‐contaminated soil

Ecotoxicology is primarily concerned with predicting the effects of toxic substances on the biological components of the ecosystem. In remote, high latitude environments such as Antarctica, where field work is logistically difficult and expensive, and where access to adequate numbers of soil invertebrates is limited and response times of biota are slow, appropriate modeling tools using microbial community responses can be valuable as an alternative to traditional single‐species toxicity tests. In this study, we apply a Bayesian nonparametric model to a soil microbial data set acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. We model community change in terms of OTUs (operational taxonomic units) in response to a range of total petroleum hydrocarbon (TPH) concentrations. The Shannon diversity of the microbial community, clustering of OTUs into groups with similar behavior with respect to TPH, and effective concentration values at level x, which represent the TPH concentration that causes x% change in the community, are presented. This model is broadly applicable to other complex data sets with similar data structure and inferential requirements on the response of communities to environmental parameters and stressors.     

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research

The Zebrafish Information Network, ZFIN, is a WWW community resource of zebrafish genetic, genomic and developmental research information (http://zfin.org). ZFIN provides an anatomical atlas and dictionary, developmental staging criteria, research methods, pathology information and a link to the ZFIN relational database (http://zfin. org/ZFIN/). The database, built on a relational, object-oriented model, provides integrated information about mutants, genes, genetic markers, mapping panels, publications and contact information for the zebrafish research community. The database is populated with curated published data, user submitted data and large dataset uploads. A broad range of data types including text, images, graphical representations and genetic maps supports the data. ZFIN incorporates links to other genomic resources that provide sequence and ortholog data. Zebrafish nomenclature guidelines and an automated registration mechanism for new names are provided. Extensive usability testing has resulted in an easy to learn and use forms interface with complex searching capabilities.     

Accumulations of Fruits and Seeds in Three Small Sedimentary Environments in Southern England and Their Palaeoecological Implications

Previous work on accumulation of plant material in modern depositionalenvironments is summarized and data from studies of three lakesediment samples, one river sediment sample and one river embaymentsurface floating sample are presented. The lake sediment sampleaway from the direct influence of an input stream but withina zone of marginal aquatic vegetation, is shown to provide themost authentic representation of the plant community withinwhich it was deposited. The sediment contained an abundant anddiverse assemblage of potential macrofossils from aquatic andmarginal aquatic plants. It also contained scant evidence ofthe existence of another plant community within the lake catchment.Details of this community were only revealed by the lake sedimentsample within the area influenced by the inflow stream. Thisand samples from other depositional environments contained confusingmixtures of potential macrofossils from local and regional vegetation.Sediment samples containing only thick walled, durable plantmaterial are considered to be the result of selective biodegradation.Under the conditions described here abrasion is considered tohave no significant effect on potential macrofossils. Variousways in which the data obtained from this study may assist inthe interpretation of plant fossil assemblages are considered. Potential macrofossils, aquatic vegetation, lake sediment, palaeoecology, fruit, seed     

秦岭天然锐齿栎林群落区系研究

锐齿栎林是秦岭林区的主要森林类型之一。通过对秦岭天然锐齿栎林群落的野外调查,报道了组成该群落的植物种类１８３种,隶属于６０科,１３１属,并在此基础上对该群落区系特点作了较为详细的分析。分析表明：１．该群落区系具有明显的温带性质。２．该群落区系是奠基在秦岭古老植物区系的基础上,通过种间竞争、群落演替形成的。３．锐齿栎本身不是一个古老的类群,其出现的时间不会早于上新世。     

Measuring the contribution of evolution to community trait structure in freshwater zooplankton

There are currently few predictions about when evolutionary processes are likely to play an important role in structuring community features. Determining predictors that indicate when evolution is expected to impact ecological processes in natural landscapes can help researchers identify eco-evolutionary ‘hotspots', where eco-evolutionary interactions are more likely to occur. Using data collected from a survey in freshwater cladoceran communities, landscape population genetic data and phenotypic trait data measured in a common garden, we applied a Bayesian linear model to assess whether the impact of local trait evolution in the keystone species Daphnia magna on cladoceran community trait values could be predicted by population genetic properties (within-population genetic diversity, genetic distance among populations), ecological properties (Simpson's diversity, phenotypic divergence) or environmental divergence. We found that the impact of local trait evolution varied among communities. Moreover, community diversity and phenotypic divergence were found to be better predictors of the contribution of evolution to community trait values than environmental features or genetic properties of the evolving species. Our results thus indicate the importance of ecological context for the impact of evolution on community features. Our study also demonstrates one way to detect signatures of eco-evolutionary interactions in communities inhabiting heterogeneous landscapes using survey data of contemporary ecological and evolutionary structure.     

Species abundance models and patterns in dragonfly communities: effects of fish predators

We investigated if dragonfly larvae community composition and species abundance curves are sensitive to variation in predation intensity, and whether the fit to a particular niche partitioning model could be used to make inferences about mechanisms structuring communities. The approach taken was to compare communities in lakes either having or lacking fish predation. Dragonfly species classified as active, strongly dominated the dragonfly communities in fishless lakes, and low active species dominated fishless lakes. As activity level is known to correlate with susceptibility to fish predation this indicates that these communities are structured by fish predation. Fitting relative abundance data to five niche partitioning models showed that the same model fitted data from both types of habitats (fish/no fish). This means that the observed differences in relative abundances were substitutive, i.e. the relative abundance of a rank stayed constant, even though the identity of the species having this rank changed. The best fit to data from both types of lakes was found for the random assortment model, which is usually interpreted as an indication that the community is not structured by within-guild interactions. This interpretation for fishless lakes did not seem to agree with other community measures (i.e. lowered diversity and evenness and no relationship between species richness and dragonfly biomass), which indicate that the community is structured by within-guild interactions. Moreover, a detail in the fitting procedure, the number of species included in the analysis, affected which model that fitted data best. Thus, we question if fitting niche partitioning models to data can provide mechanistic understanding of how resources are partitioned in natural communities.     

Phylogenetic analysis of community assembly and structure over space and time

Evolutionary ecologists are increasingly combining phylogenetic data with distributional and ecological data to assess how and why communities of species differ from random expectations for evolutionary and ecological relatedness. Of particular interest have been the roles of environmental filtering and competitive interactions, or alternatively neutral effects, in dictating community composition. Our goal is to place current research within a dynamic framework, specifically using recent phylogenetic studies from insular environments to provide an explicit spatial and temporal context. We compare communities over a range of evolutionary, ecological and geographic scales that differ in the extent to which speciation and adaptation contribute to community assembly and structure. This perspective allows insights into the processes that can generate community structure, as well as the evolutionary dynamics of community assembly.