Pluralism and diversity: trends in the use and application of ordination methods 1990‐2007

Question: What are the trends and patterns in the application of ordination techniques in vegetation science since 1990? Location: Worldwide literature analysis. Methods: Evaluation of five major journals of vegetation science; search of all ISI‐listed ecological journals. Data were analysed with ANCOVAs, Spearman rank correlations, GLMs, biodiversity indices and simple graphs. Results: The ISI search retrieved fewer papers that used ordinations than the manual evaluation of five selected journals. Both retrieval methods revealed a clear trend in increasing frequency of ordination applications from 1990 to the present. Canonical Correspondence Analysis was far more frequently detected by the ISI search than any other method. Applications such as Correspondence Analysis/Reciprocal Averaging and Detrended Correspondence Analysis have increasingly been used in studies published in “applied” journals, while Canonical Correspondence Analysis, Redundancy Analysis and Non‐Metric Multidimensional Scaling were more frequently used in journals focusing on more “basic” research. Overall, Detrended Correspondence Analysis was the most commonly applied method within the five major journals, although the number of publications slightly decreased over time. Use of Non‐Metric Multidimensional Scaling has increased over the last 10 years. Conclusion: The availability of suitable software packages has facilitated the application of certain techniques such as Non‐Metric Multidimensional Scaling. However, choices of ordination techniques are currently less driven by the constraints imposed by the software; there is also limited evidence that the choice of methods follows social considerations such as the need to use fashionable methods. Methodological diversity has been maintained or has even increased over time and reflects the researcher's need for diverse analytical tools suitable to address a wide range of questions.     

我国植被数量分析方法的研究概况和发展趋势

植被数量分析是现代植被研究的重要手段,数量分类和排序是现代植被生态学研究最重要的,也是应用最广泛的生态学技术。数量分析方法在20世纪50年代引入植被生态学研究领域,我国学者在70年代后期开始研究植被的数量分类和排序。本文主要从相关资料、应用研究、新方法研究三个方面论述了我国植被数量分析方法的发展,重点阐述了从20世纪70年代后期以来出现的并且被广泛应用的新方法及其应用研究概况,并在此基础上分析了植被数量分析方法未来的发展趋势。     

瑞典河漫滩草甸植被的数量分类和排序

本文用目前各国学者广泛使用的一些数量分类和排序方法对瑞典河漫滩草甸样地资料进行了分类和排序。所用的方法包括多元等级聚合分类(TABORD程序),多元等级分划分类(TWINSPAN程序),PCA排序(ORDINA程序),RA和DCA排序(DECORANA程序)。研究结果表明可以把28个样地分为6个群落类型,它们的分布格局是与土壤水分梯度密切相关的。此外本文还对数量分类和排序方法在植物群落学研究中的应用以及所用方法的比较进行了讨论。     

微生物生态研究中BIOLOG方法数据分析及R语言实现

微生物生态研究中,对微生物群落结构、群落特征以及其与环境因素的关系的揭示,一直受到广泛关注;适当的数据分析方法有助于更清晰地刻画微生物群落结构特征,明确其与环境因素的关系。结合实例,对微生物生态研究中基于BIOLOG微平板技术的数据分析方法进行梳理,分别介绍数据读取整理、特征指数计算、非限制性排序、限制性排序、聚类分析、环境向量拟合、蒙特尔检验等常用数据操作及生态分析方法;针对不同方法结论,结合研究目标和生态理论给出具有统计学意义的解释,并评价不同方法特点及适用场景;分析过程以R语言实现,并提供全部代码。结果表明,BIOLOG方法产生数据能从多个角度表征微生物群落功能特征,并结合环境指标梯度进行分析;但BIOLOG数据可能不满足正态性分布,在基于正态分布的分析前应提前进行检验;排序分析时应慎用主成分分析,可优先采用其他基于距离矩阵的排序方法;R语言能够简化BIOLOG数据读取及操作,易于完成各类统计分析。本研究能够对微生物生态研究者科学选择应用统计分析方法、提高数据处理效率提供直接参考。     

The development of numerical classification and ordination

Summary The paper reviews the constraints and influences which have affected the development of numerical classification and ordination of vegetation.Initial development of ordination techniques and their reception by ecologists was hindered by the mistaken idea that ordination involved acceptance of variation in vegetation as a continuum, as well as by a general suspicion of mathematical approaches.Three distinct approaches to ordination, largely unrecognised at the time, are apparent in earlier work: direct gradient analysis, reduction in dimensionality and path-seeking (catenation) (Dale 1975).Modifications of simple initial techniques made them more efficient at the cost of increased computation. Acceptance of heavier computation as computers increased in capacity and speed turned attention to prineipal component analysis and the superficially similar factor analysis. These have been widely misunderstood largely because they were initially applied in the same way as in the analysis of psychological data, in which different constraints and objectives apply. The initial failure to recognise that principal component analysis involves a preliminary data transformation, the form of which depends on answers to biological, not mathematical, questions, was particularly unfortunate.Principal component analysis has limitations as a technique of ordination resulting from its assumptions of linearity and additivity of plant responses. Attempts to devise more effective techniques raise questions about the practical importance of non-linearity if the objective is data-exploration rather than elucidating the nature of species-response curves and about the adequacy of using simulated data as test data when we do not know how to simulate realistic data.Data-exploration has been more prominent in practical uses of ordination but many methodological developments have concentrated rather on species-response curves.Numerical classification also met obstacles to its acceptance additional to a general aversion to numerical techniques. The first numerical techniques were presented in the context of the relationships of a particular set of data, rather than of a generally valid system, which was the more familiar concept in non-numerical classification.Both numerical and non-numerical classification aim to produce as homogeneous groups as possible. The distinctive contribution of numerical methods is to allow the data to indicate the most efficient criteria of classification; this was an unfamiliar idea.The strategy of classification may be either divisive or agglomerative and either monothetic or polythetic. Choice of strategy in earlier work was not only constrained by computational limitation but may also have been influenced by an author's previous experience of non-numerical classification. As with ordination, the distinction between preliminary data transformation and subsequent analysis was at first not appreciated.Numerical classification has been influenced by parallel numerical developments in formal taxonomy. Because objectives and assumptions are not always the same, this influence has not been altogether helpful.The limitations of real data suggest that developments of technique are at risk of becoming too concerned with refinements of methodology. Increasingly complex methods and increasing availability of programmes for such methods carry the risk that they may be used without adequate understanding of what they do.     

A comparison of detrended correspondence analysis and principal co-ordinates analysis using four sets of Tasmanian vegetation data

Indirect gradient analysis, which entails the elucidation of relationships between trends in community composition and underlying environmental or successional gradients, is a major objective of ordination in plant ecology. Two ordination techniques, detrended correspondence analysis (DCA) and principal co-ordinates analysis (PCOA), were compared using three sets of Tasmanian vegetation data having known gradients and one set where the vegetation was expected to respond to diverse environmental variables. In every case, the results obtained by DCA were considered superior to, or at least as good as, those of PCOA. Hence, DCA appears to be the more suitable of the two methods for indirect gradient analysis.     

排序法在植物群落与环境关系研究中的应用述评

自然环境对植物的影响主要表现在气候、水文、土壤及地形方面。大尺度上,气候类型明显影响植物的带状分布与物种空间格局;中小尺度上,土壤、水文、地形以及三者的交互作用影响植物生长必需的环境与资源条件,并对植物群落物种多样性起决定性作用。多元数量分析是研究植物群落生态关系的重要方法,在揭示植物群落与环境关系方面起到关键作用。排序法作为数量分析的重要手段,经常在植物生态学研究中扮演重要角色,尤其是在植物群落分布以及群落结构方面的应用已形成一种趋势。主要从植物群落分布以及群落结构的角度综述了当今排序法的应用,分析了面临的主要问题,并提出了未来可能发展方向,以期为今后排序方法的选择应用提供参考。     

Plant community and landscape patterns of a floodplain wetland in Maputaland, Northern KwaZulu-Natal, South Africa

The lower Mkuze River floodplain is located east of the Lebombo Mountains on the Maputaland Coastal Plain in northern KwaZulu‐Natal, South Africa. The vegetation ecology of the floodplain was examined using the hierarchical framework described by landscape ecology theory. The smallest spatial scale to which the vegetation of the floodplain was described was the relatively homogeneous units of plant communities. From a landscape ecology perspective this level of analysis is referred to as the grain. Six plant communities were identified using two‐way indicator species analysis (TWINSPAN) classification. The distribution of these plant communities were correlated to an underlying inundation‐sedimentation gradient using the ordination technique, detrended correspondence analysis (DCA). This correlation provided a useful foundation for the examination of ecological processes and phenomena at the next higher, spatially coarser level within the landscape hierarchy, namely the reference level. This reference level was described by three functional types delimited by differing flooding and sedimentation regimes. The use of landscape ecology theory guided the interpretation of results by explicitly recognizing the importance of spatial heterogeneity, hierarchical organization and dynamics, and proved invaluable in developing process‐based understanding of the vegetation ecology of the lower Mkuze River floodplain.     

中条山中段植物群落数量分类与排序研究

在群落样方调查基础上,采用双向指示种分析法（TWINSPAN）和除趋势对应分析（DCA）对中条山中段植物群落进行了数量分类和排序。TWINSPAN将53个样方分为14组,根据植被分类的原则划分为14个群丛,论述了各群丛的群落学特征。53个样方的DCA排序结果反映了植物群落类型与环境梯度之间的关系,表明影响群丛分布格局的主导生态因子为海拔高度、水分和热量。DCA排序将65个种分为5个种组,各种组在排序轴上的位置反映了种组成员的生态适应性及其在群落中的重要性和更新生态位。     

Mapping the floristic continuum: Ordination space position estimated from imaging spectroscopy

Objective: To present a non‐classificatory technique of map representation of compositional patterns of vegetation as no two plant species assemblages are completely alike and gradations often occur. Variation is depicted as continuous fields instead of classes. Location: Murnauer Moos, Bavaria. Methods: The study combined vegetation ecology and remote sensing methods. The gradual representation of compositional patterns was based on techniques of ordination and regression, instead of mapping class fractions. The floristic field data were collected in relevés and subjected to three‐dimensional non‐metric multidimensional scaling (NMS). The reflectance information corresponding to plots was gathered from remotely sensed imagery with a high spectral resolution. Reflectance values in numerous wavelengths were related to NMS axes scores by partial least squares regression analysis. The regression equations were applied to the imagery and yielded three grey‐scale images, one for each ordination axis. These three images were transformed into a red, green, and blue colour map with a specific colour for each position in the ordination space. Similar colours corresponded to similar species compositions. Results: Compositional variation was mapped accurately (R²= 0.79), using continuous fields. The results took account of various types of stand transitions and of heterogeneities within stands. The map representation featured relatively homogeneous stands and abrupt transitions between stands as well as within‐stand heterogeneity and gradual transitions. Conclusions: The use of NMS in combination with imaging spectroscopy proved to be an expedient approach for non‐classificatory map representations of compositional patterns. Ordination is efficiently extended into the geographic domain. The approach in abandoning pre‐defined plant communities is able to reconcile mapping practice and complex reality.     

Modelling Environmental Responses of Plant Associations: A Review of Some Critical Concepts in Vegetation Study

The definition of vegetation types at different hierarchical levels, both to study the vegetation processes and for practical cartographic representation, is still considered a critical issue in many circles of plant ecologists. The problems are mainly related to the misleading idea that classification of the vegetation system, as developed by European phytosociologists during the last century within the discipline called syntaxonomy, would imply the assumption of the organismic concept of the plant community. After a short discussion on the role of Braun-Blanquet approach in plant ecology and in landscape ecology, the methods to detect multispecies responses along environmental gradients are briefly reviewed. In the main part of this article, we intend to stress that concepts considered critical, such as plant association and its ecological niche, are just operational tools that have nothing to do with the individualistic or organismic interpretation of plant communities in vegetation studies. Important to our views on vegetation, we believe that plant associations as well as the higher syntaxa can be regarded as fuzzy sets in an operational context for describing vegetation along ecological gradients in synthetic ways and can further the understanding of vegetation variation.     

庞泉沟自然保护区华北落叶松林的自组织特征映射网络分类与排序

自组织特征映射网络（SOM）是新近引入植物生态学的分析方法,对复杂问题和非线性问题具有较强的分析和求解功能。本研究应用SOM分类和排序研究了庞泉沟自然保护区华北落叶松林。研究结果表明,SOM将120个样方分为7个植物群落类型,分类结果具有明确的生态意义;样方和物种在SOM训练图上呈现一定规律的分布;7个群落类型各有其分布范围和界限,揭示了群落间的生态关系。在此基础上,通过引入一种在SOM训练图上可视化环境因子梯度的方法,能够较好地完成样方、物种和环境因子相互关系的分析,揭示了海拔是影响该区华北落叶松林生长和分布的最主要因子。生态分析表明SOM分类和排序是一种有效的梯度分析方法,适用于表征生态特征和探索群落和环境相互关系的研究。     

The origins and detection of plant community structure: Reproductive versus vegetative processes

The exchange of ideas and information between vegetation ecology and pollination ecology is relatively restricted, yet both fields have devised methods to detect the structure of species assemblages and communities. To promote the exchange of ideas between fields I compare approaches, concepts, and problems faced by researchers working in each area. Both vegetative and reproductive interactions may generate assemblage structure through ecological sorting or through character displacement. Vegetative interactions may lead to assemblage organization more often by ecological sorting and reproductive interactions more often by character displacement. Vegetative interactions generally operate over shorter temporal and smaller spatial scales than reproductive interactions and may be affected more strongly by temporal and spatial heterogeneity in abiotic and biotic environments. These differences affect how the concept of ecological niche should be applied to plants. The Hutchinsonian concept of niche needs to be significantly modified before it can be usefully applied to plants. Null models are a valuable tool for investigating both vegetative and reproductive structuring of plant assemblages; however, the procedures followed in the application of null models need further refinement. The appropriate formulation of the null model may require information that is unavailable, hence multiple models may have to be employed to “bracket” conclusions. The literature on pollination community ecology demonstrates that difficult decisions must be made about the likely processes that have generated the structure being tested, the relevant definition of sympatry, how guid membership should be defined and employed, and what constraints should be incorporated into the null model to impose realism. Differences in these decisions will affect the outcome of the analysis. While top-down studies of pattern have numerous advantages, they usually cannot identify the process(es) that have generated the patterns. Bottom-up, experimental studies can be useful for identifying the processes, but they can rarely be used to assess the structure of an entire natural assemblage. The optimal approach to studying assemblage structure is to detect patterns with top-down analysis and use experiments to identify the processes that generate and maintain the patterns.     

Quantitative classification and ordination of forest communities in Pangquangou National Nature Reserve

Quantitative analysis of ecological relationships between vegetation and the environment has become an essential means in the field of research of modern vegetation ecology. In this article, based on data from 84 quadrates, forest communities in this reserve were investigated using TWINSPAN, DCA and DCCA. The results will be helpful in the construction and development of Pangquangou National Nature Reserve. Using TWINSPAN, the forest communities were classified into seven types. The distribution pattern of vegetation reflects the comprehensive influence of environments. The results of DCA and DCCA clearly reflect the relationship between the pattern of forest communities and environmental gradients. The ordination result of DCCA indicates that altitude is more important than other environmental factors because the change of altitude gradient will lead to changes in the temperature and humidity gradients. The first of the DCA ordination axes indicates the humidity gradient, and the second indicates the temperature gradient. All these results show that the main factors restricting the distribution of communities in this reserve are temperature and humidity. The ecological meaning of the ordination axis in DCCA is much clearer than that in DCA, and the species-environment correlation of DCCA is more obvious than DCA. The first DCCA axis indicates the altitude gradient among the communities, while the second is the gradient in aspect and slope among the communities. DCCA ordination can simultaneously express similarities of species and environment. Therefore, the quadrat location in the DCCA ordination figure is much closer than in the DCA.     

Quantitative classification and ordination of forest communities in Pangquangou National Nature Reserve

Quantitative analysis of ecological relationships between vegetation and the environment has become an essential means in the field of research of modern vegetation ecology. In this article, based on data from 84 quadrates, forest communities in this reserve were investigated using TWINSPAN, DCA and DCCA. The results will be helpful in the construction and development of Pangquangou National Nature Reserve. Using TWINSPAN, the forest communities were classified into seven types. The distribution pattern of vegetation reflects the comprehensive influence of environments. The results of DCA and DCCA clearly reflect the relationship between the pattern of forest communities and environmental gradients. The ordination result of DCCA indicates that altitude is more important than other environmental factors because the change of altitude gradient will lead to changes in the temperature and humidity gradients. The first of the DCA ordination axes indicates the humidity gradient, and the second indicates the temperature gradient. All these results show that the main factors restricting the distribution of communities in this reserve are temperature and humidity. The ecological meaning of the ordination axis in DCCA is much clearer than that in DCA, and the species-environment correlation of DCCA is more obvious than DCA. The first DCCA axis indicates the altitude gradient among the communities, while the second is the gradient in aspect and slope among the communities. DCCA ordination can simultaneously express similarities of species and environment. Therefore, the quadrat location in the DCCA ordination figure is much closer than in the DCA.     

环境DNA技术在地下生态学中的应用

地下生态过程是生态系统结构、功能和过程研究中最不确定的因素。由于技术和方法的限制,作为"黑箱"的地下生态系统已经成为限制生态学发展的瓶颈,也是未来生态学发展的主要方向。环境DNA技术,是指从土壤等环境样品中直接提取DNA片段,然后通过DNA测序技术来定性或定量化目标生物,以确定目标生物在生态系统中的分布及功能特征。环境DNA技术已成功用于地下生态过程的研究。目前,环境DNA技术在土壤微生物多样性及其功能方面的研究相对成熟,克服了土壤微生物研究中不能培养的问题,可以有效地分析土壤微生物的群落组成、多样性及空间分布,尤其是宏基因组学技术的发展,使得微生物生态功能方面的研究成为可能;而且,环境DNA技术已经在土壤动物生态学的研究中得到了初步应用,可快速分析土壤动物的多样性及其分布特征,更有效地鉴定出未知的或稀少的物种,鉴定土壤动物类群的幅度较宽;部分研究者通过提取分析土壤中DNA片段信息对生态系统植物多样性及植物分类进行了研究,其结果比传统的植物分类及物种多样性测定更精确,改变了以往对植物群落物种多样性模式的理解。同时,环境DNA技术克服传统根系研究方法中需要洗根、分根、只能测定单物种根系的局限,降低根系研究中细根区分的误差,并探索性地用于细根生物量的研究。主要综述了基于环境DNA技术的分子生物学方法在土壤微生物多样性及功能、土壤动物多样性、地下植物多样性及根系生态等地下生态过程研究中的应用进展。环境DNA技术对于以土壤微生物、土壤动物及地下植物根系为主体的地下生态学过程的研究具有革命性意义,并展现出良好的应用前景。可以预期,分子生物学技术与传统的生态学研究相结合将成为未来地下生态学研究的一个发展趋势。     

排序和广义线性模型与广义可加模型在植物种与环境关系研究中的应用

排序和广义线性模型(Generalized Linear Model,GLM)与广义可加模型(Goneralized Additive Model,GAM)是研究植物种与环境间关系的重要方法。基于线性模型的排序方法应限定于环境梯度较短的植被数据。而基于单峰模型的排序方法更适用于梯度较长的情况。PCA、CA／RA系列和CCA系列是常用的排序方法。同时进行环境数据和植被数据分析的CCA系列,能清楚地得出植物种与环境间的关系。CCA改进后的DCCA和PCCA,是现今较理想的排序方法。GLM和GAM实质上是用环境变量的高阶多项式来拟合植物种与环境变量的关系。GLM和GAM扩展了植物种与环境变量之间的关系模型,能深入地探讨植物种与环境间的关系。GLM主要是模型决定的,而GAM主要取决于原始数据。一般来说,排序能得出研究区域的主要环境梯度,提供了物种聚集和植物群落的概略描述。GLM与GAM对于深入研究单个植物种与环境间的关系具有优势。在实际研究中,两种方法结合使用能互补不足。     

丛枝菌根真菌与深色有隔内生真菌生态修复功能与作用

生态修复是目前全球关注的热点问题,如何增加植被的覆盖度及生态修复效率是目前研究的重点。丛枝菌根真菌(arbuscular mycorrhiza fungi,AMF)和深色有隔内生真菌(dark septate endophyte,DSE)均是自然界植物根际分布广泛的一类内生真菌,均能与植物形成菌根共生体,具有一定的促进植物生长、抵抗逆境及修复污染土壤等功能与作用,在生态修复中具有广泛的应用潜力。本文综述了AMF及DSE两种微生物的功能、作用及其在生态修复应用中的研究进展,并进一步对AMF和DSE在生态修复中存在的问题和前景进行展望。     

Classification of vegetation: Past,present and future

Abstract. This paper is a report on the past, status-quo and perspectives of vegetation classification, still a major occupation of many vegetation scientists. The history of vegetation classification is discussed against a background of several controversial issues such as the problem of continuum vs. discontinuum, naturalness vs. arbitrariness of the nature of plant communities, universality vs. ad hoc character of syntaxonomic schemes, as well as classical versus numerical approaches to data analysis for classification purposes. The development of the methodology of vegetation science and the present image of vegetation classification is documented by a bibliometric analysis of the publication record of four majorjournals: Journal of Vegetation Science, Vegetatio, Phytocoenologia and Tuexenia. This analysis revealed a persisting controversy between traditional and numerical approaches to vegetation classification. A series of important changes in vegetation science (foundation of new journals, change of editorial policy by the established, important meetings) punctuate a period called the ‘Innovation period’. Several trends in the development of methods of vegetation systematics are summarized under the headings formalism, pluralism, functionalism, pragmatism and indeterminism. Some new features, such as the development and improvement of numerical tools, use of large data banks and attempts to summarize the theory of vegetation classification are discussed. The new growth-form system of Barkman initiated a revival of physiognomy-based vegetation classification. Within this framework the use of the character-type concept and the development of new numerical methods for studying the hierarchical structure of character-set types seems to be a promising approach. The achievements of population biology and ecophysiology have affected vegetation science by emphasizing the functionality of species within plant communities. The use of guilds and other functional groups has experienced an increasing interest from vegetation scientists. Applied in vegetation science, fuzzy-set theory has bridged the techniques of classification and ordination of plant communities.