Correspondence Analysis of species by environmental variable matrices

Abstract. Correspondence Analysis of species by environmental variables matrices is a relatively simple method for handling matrices which include many species and variables. If columns represent species and rows represent the states in which the environmental variables have been divided, each element of the matrix shows the number of releves in which the simultaneous occurrence of that species and that environmental variable state have been recorded. In this paper the use of the method for presence-absence data is considered. The method is appropriate for studies whose main purpose is to look for broad correlations between groups of environmental variables and groups of species. It is particularly useful for handling heterogeneous data sets including rare species and species-poor releves, a situation in which Correspondence Analysis and Canonical Correspondence Analysis are frequently complicated by the production of axes explaining the relationship between rare species and species-poor releves. Examples are presented with artificial data as well as with real data collected in the Mexican portion of the Chihuahuan Desert (Bolsón de Mapimi). It is shown for the Mapimi data that the method is robust to the partition of variables into different numbers of states.     

典范指示种分析— 一个新的外在分类方法

 本文描述一个新的外在分类方法—典范指示种分析。它是以典范对应分析排序轴为基础,同时使用植被数据和环境数据,其结果能更好地反映植被与环境的关系。我们用该方法对英国威尔士北部山地草甸的数据进行了分析,结果证明它是较理想的分析方法。     

A new dissimilarity measure and a new optimality criterion in phytosociological classification

A new dissimilarity measure, Uppsala dissimilarity, is proposed. It is a Manhattan-type measure in between the Canberra and Gower measures, based on the differences between scores in relevés compared, but it also takes both the sums of scores and the difference between maximum and minimum score into account. The measure is considered realistic for phytosociological material.A new optimality criterion has been developed after unsatisfactory results had been obtained with the DOL criterion (Popma et al. 1983) which was developed previously by our group. Problems with DOL were especially met when the criterion was applied to the distribution of only one species over the cluster array obtained. The new criterion takes both internal cluster homogeneity and between-cluster dissimilarity into account. Between-cluster dissimilarity is calculated for all other clusters and not only for the nearest neighbour, as in DOL. The new criterion has both an unweighted form: SOM, and a form with weighting for cluster size: SWOM.This new criterion was successfully applied to the evaluation of the sharpness of distribution of individual species over cluster arrays, under the name of SIM: species indication measure and SWIM, species weighted indication measure.The measures were applied to some test data. Differences between the unweighted and weighted forms were found which could not be easily interpreted.Some remarks are made on the coherence of d-SAHN and h-SAHN approaches in agglomerative clustering within the new strategy proposed.Abbreviations DOL = Detection of Optimal Level - S(W)IM = Species (Weighted) Indication Measure - S(W)OM = Standardized (Weighted) Optimality Measure - UD = Uppsala Dissimilarity measure - WPGMA = Weighted Pair-Group Method Average linking clustering - SAHN = Sequential Agglomerative Hierarchical Non-overlapping clustering     

A comparison of three methods of multivariate analysis of upland grasslands in North Wales

Abstract. In a study of the relationships between vegetation and environment in North Snowdonian grasslands, 166 quadrats on 10 altitudinal transects were analysed with Detrended Correspondence Analysis, Detrended Canonical Correspondence Analysis and Fuzzy Set Ordination. These techniques provide consistent results. DCCA and FSO, both using floristic community data and environmental information, simplify the procedure of vegetation-environment analysis. FSO analyses and synthesizes ecological information; it may yield more reasonable and interpretable results.     

Plant communities of New Brunswick in relation to environmental variation

Abstract. The objective of this study was to quantitatively describe vegetation-environment relationships at a regional scale within the Province of New Brunswick, Canada, using vegetation and environment data from 3947 provincial forestry sample plots. The major plant community types in the province were identified using cluster analysis. Relationships of these communities to climate, topography and soil variables were analyzed by Canonical Correspondence Analysis (CCA), using both a reduced data set consisting of cluster likelihood scores × sample plots and an unreduced species × sample plots data matrix. The vegetation types and major axes of environmental variation were mapped to examine the geographic distributions of these factors within the province. Eight communities were identified and described in terms of enhanced/reduced species (significantly higher or lower frequencies of occurrence in a specific community type relative to all plots) and common species (species in the community type with the highest frequencies of occurrence). The canonical axes explained 25 % of the variation in the vegetation cluster data. Vegetation composition was related to three major environmental gradients representing climate and elevation, soil moisture, and soil fertility. The geographic distributions of vegetation communities exhibited predictable but weak correspondence to the geographic distributions of individual environmental factors. Our findings emphasize the overriding importance of climate and topography and the secondary importance of soil factors in controlling vegetation pattern at the regional scale.     

Plant community structure in an oligohaline tidal marsh

An oligohaline tidal marsh on the northern shore of Lake Pontchartrain, LA was characterized with respect to the distributions and abundances of plant species over spatial and temporal gradients using Detrended Correspondence Analysis (DCA). In addition, the species distributions were correlated to several physical environmental factors using Detrended Canonical Correspondence Analysis (DCCA). The distributions of species were best correlated with distance from Lake Pontchartrain, and to a lesser extent with elevation and substrate organic matter. They were least correlated with mean soil salinity (referred to here as background salinity). Of the three mid-seasonal dominant species, the perennial grass, Spartina patens, is the most salt tolerant and was found closest to the lake. Further inland the dominant perennial was Sagittaria lancifolia, which has a salt tolerance less than that of Spartina patens. The perennial sedge, Cladium jamaicense, which is the least salt tolerant of the three, was dominant furthest inland. Background salinity levels were generally low (<5 ppt.) and did not explain species distributions. We hypothesize that the distribution of species is regulated by occasional storm-generated salt pulses that generate strong, short-lived salinity gradients as a function of distance from the lake. Biotic interactions likely also play a role in structuring the plant community. The distributions of several annuals depended on the size and life history of the mid-seasonal dominant perennials. Most of the annuals frequently co-occurred with Sagittaria lancifolia, which was the shortest in stature and had the least persistent canopy of the three mid-seasonal dominant perennials.Abbreviations DCA Detrended Correspondence Analysis - DCCA Detrended Canonical Correspondence Analysis     

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.     

雅鲁藏布江河岸植物物种丰富度分布格局及其环境解释

沿环境梯度物种多样性的分布格局及其环境影响因子的研究是生态学研究的重点内容之一。雅鲁藏布江是我国海拔最高的大河, 目前还没有针对其流域的河岸植物群落物种丰富度分布格局的系统研究。作者沿海拔梯度从雅鲁藏布江上游源头区至下游共设置了15个海拔样带, 在每个海拔样带随机取6个5 m×5 m样方, 共对90个样方的河岸植物群落物种组成和植被类型进行了调查, 共记录到238种维管束植物。DCA排序结果表明物种组成变化主要受海拔和经度控制。CCA排序区分出5种大的植被类型, 即高寒草甸或高寒草原、高山草原、两种亚高山灌丛草原和林缘灌丛植被。各植被类型的分布和变化主要受海拔和经度影响。雅鲁藏布江河岸植物物种丰富度沿海拔和经度梯度呈浅“U”形分布格局, 物种丰富度与年均降水量和植被盖度成显著正相关。     

Above-ground biomass and species richness in a Mediterranean salt marsh

Abstract. Species composition, above-ground biomass and diversity of herbaceous communities were recorded in 50 sites on the upper salt marsh of the Guadalquivir delta (SW Spain). Through Canonical Correspondence Analysis relationships were shown between plant-species characteristics abundance and environmental variables. Seven community types were distinguished and related to hydro logical regime and physical and chemical soil parameters. The higher species richness was associated with moderate values of above-ground biomass (Biomass at maximum diversity, BMD = 302 g/m²). Salinity was negatively correlated with species richness. There was no significant correlation with total above-ground biomass. Water regime and soil nutrient (Ca, Mg) content were significant predictors of the community above-ground biomass.     

Two-step vegetation analysis based on very large data sets

A two-step method for the classification of very large phytosociological data sets is demonstrated. Stratification of the set is suggested either by area in the case of a large and geographically heterogeneous region, or by vegetation type in the case of a set covering all the plant communities of an area. First, cluster analysis is performed on each subset. The resulting basic clusters are summarized by calculating a ‘synoptic coverabundance value’ for each species in each cluster. All basic clusters are then subjected to the same procedure. Second order clusters are interpreted as community types. The synoptic value proposed reflects both frequency and average cover-abundance. It is emphasized that a species should have a high frequency to be used as a diagnostic species. The method is demonstrated with a set of 1138 relevés and 250 species of coastal sand dune vegetation in Yucatan treated with the programs TWINSPAN and TABORD. Some problems and perspectives of the approach are discussed in the light of hierarchy theory and classification theory.     

Population structure and environmental relationships of the tropical tree Nectandra rudis (Lauraceae), a rare species in western Mexico

Population structure and environmental relationships of the tropical tree Nectandra rudis (Lauraceae), a rare species in western Mexico. The tree N. rudis is a rare species from western Mexico of which community and population features are unknown. We studied a population in an altitudinal gradient, from 550-1,850 m above sea level in the Sierra de Manantlan, Jalisco, Mexico. We established four 60x48 m sample sites at vertical distances of 100 m along this altitudinal gradient. Within each plot, ten 100 m2 circular sub-sampling units were randomly located. At each unit, we recorded diameter at breast height (dbh) and tree height for all woody vegetation > or =2.5 cm dbh. Basal area, tree density, frequency, species richness and importance values per species and plot. We estimated the vertical structure (total tree height) and diameter( as M=5log(10)N) for all N. rudis individuals. A direct ordination through Canonical Correspondence Analysis was done, involving amongst other species, edaphic and environmental data matrices. The record of 44 N. rudis individuals, in seven out the 56 plots sampled, represents the most septentrional record for the species and the first in Western Mexico. Its density and basal area represented 4.5 % and 8.7 % respectively of the total estimated for the community. The greatest importance values were observed at 1 650 m above sea level. The population structure of N. rudis is structured into five diameter categories in an inverse "J" shaped distribution. This is a typical behavior observed to occur in the Lauraceae, which produces big seeds of short viability that germinate when there is high soil moisture content. The species tend to form dense seedling banks although only a reduced number of them are able to survive. Species richness varies from 27 to 39 at plot level; the greatest importance values for the plots on which N. rudis was found, corresponds to Urera verrucosa (Liebm.) V.W. Steinm., N. rudis, Ficus sp., Beilschmiedia manantlanensis Cuevas y Cochrane, amongst others. Canonical Correspondence Analysis suggests that environmental variables such as rooted trees, crown cover, litter depth and soluble magnesium are the more significant explanatory variables for the distribution and abundance of N. rudis.     

Factors influencing spatial distribution of fish communities on a fringing reef at Mauritius, S.W. Indian Ocean

This paper analyses the spatial patterns of fish communities on a narrow fringing reef of Mauritius and identifies some controlling factors. Canonical Correspondence Analysis revealed that the location in the reef ecosystem, the living coral coverage, and the proximity to a dredged area were the major factors controlling the distribution and abundance of fish species. Two distinct communities were observed across the fringing reef, representing a land-ocean gradient. The low diversity of fish species, and also of invertebrates such as corals, molluscs, and echinoderms is probably a consequence of the narrowness of the fringing reef and of anthropogenic impacts, notably the high pollution by nutrients.     

北部湾北部生态系统结构与功能——浮游动物空间生态位及其分化

根据2006—2007年北部湾北部海域4个航次调查资料,采用K-优势度曲线法对浮游动物种(类)群进行排序分析,运用Levins公式和Pianka指数分析了主要优势种(类)群的生态位宽度值和生态位重叠程度,并通过除趋势典范对应分析(DCCA)研究生态位分化状况。结果表明,该海区浮游动物优势种(类)群按生态位宽度值可划分为广生态位、中生态位和窄生态位三大类型。其中,广生态位的种(类)群如肥胖软箭虫、亚强次真哲水蚤、长尾类幼体等具有较强的生态适应性,生活范围较广;窄生态位的种(类)群,对环境的适应性较差,对海流和水团等环境因素的变化具有指示意义。生态位宽度能够反映种(类)群丰度季节变化,但不能反映具体丰度大小。北部湾北部全年主要优势种(类)群的生态位宽度值介于0.08—0.77之间,并且各优势种(类)群的生态位宽度差异较大,种对间生态位重叠值介于0.02—0.89之间,平均生态位重叠指数为0.45,种(类)群之间利用资源环境的互补性较强,这与海域内生境多样化并且各优势种对环境适应能力的差异存在一定联系。DCCA分析表明,影响浮游动物分布的主要因子是水深、温度和盐度,其次是叶绿素a和溶解氧。     

Vegetation in Danish beech forests: the importance of soil,microclimate and management factors,evaluated by variation partitioning

The importance of management regime on floristic variation (mosses and vascular plants) in four Danish beech forests was investigated. Sixty-four blocks were sampled, representing beech stands of different age and management types. Nineteen potential explanatory variables were recorded and tested with Monte-Carlo tests and Canonical Correspondence Analysis. In addition results were evaluated by use of Detrended Correspondence Analysis. Explanatory variables were divided into three groups; soil, microclimatic and management parameters. The amount of variation explained by each group of variables was calculated by use of variation partitioning. The group consisting of management variables explained most variation, on local as well as regional scale. Management related variables explained more variation in vegetation than any other variables together. This indicates the importance of management as determining species composition in Danish beech forests. Management related variables explained most variation on local scale. On a regional scale, soil parameters explained the major part of the variation. The results suggest that thirty years without management are sufficient to change species composition significantly, as compared to managed forests.     

Trends in structural compositional attributes of dune-interdune vegetation and their edaphic relations in the Indian desert

Vegetation of 127 sites on different aspects of dune-interdunes in the Indian Thar Desert was classified using TWINSPAN. TWINSPAN groupings of sites separated better vegetated dunes of the northeast form the poorly vegetated dunes of the northwest and the southwest. Of the different ordinations using noncentred, centred and centred and standardized principal component analysis, reciprocal averaging and detrended correspondence analysis (DCA), the site and species classes in DCA correlated well with ten edaphic and ten vegetational attributes of each site. Strong correlation of vegetation groupings with soil texture, moisture holding capacity and low correlation with pH and electrical conductivity revealed the possible importance of soil physical properties in affecting vegetation composition.The 11 species classes in TWINSPAN were regrouped into 18 species classes in DCA, which separated highly frequent species from those of less and least frequent species. Based on dominance-diversity attributes, Calligonum polygonoides-Lasiurus sindicus was brought out as bioedaphic climax stage. Correlation of ordination scores in different site groupings with vegetational attributes showed specific trends: From the zero of x, y and z axes to their maximum, the ordination scores of grasses and browse species declined while score of spinous species increased. The sites near the origin of the x, y and z axes were therefore least degraded and those at or near the maximum of x, y & z axes were most disturbed as was confirmed by the dominance diversity trends. Thus trends of compositional and functional attributes of vegetation of sites in different groupings helped in inferring a site's degradation status.Abbreviations RIV Relative importance value - TWINSPAN Two Way Indicator Species Analysis - PCA Principal Component Analysis - RA Reciprocal Averaging - DCA Detrended Correspondence Analysis - EC Electrical Conductivity - WHC Water Holding Capacity - BD Beta Diversity - DC Dominance Concentration - WWS Windward slope of the dune - LWS Leeward slope of the dune - ID Interdune Nomenclature: Bhandari, (1990)     

A combination of fuzzy set ordination with detrended correspondence analysis: One way to combine multi-environmental variables with vegetation data

This paper examines one possible way of Fuzzy Set Ordination by using multi-environmental variables. FSO's function is improved through combination with Detrended Correspondence Analysis which is used to summarize environmental information. It can be used to analyse the relationships between vegetation and environment no matter how many environmental variables are involved. An example with vegetation and environmental data collected from upland grasslands in Northern Snowdonia, Wales, is presented. Its results are consistent with that of CCA and DCCA.Abbreviations FSO Fuzzy set ordination - DCA Detrended correspondence analysis - CCA Canonical correspondence analysis - DCCA Detrended canonical correspondence analysis     

我国入侵植物多样性的区域分异及其影响因素——以74个地区数据为基础

以我国74个地理单位282种外来入侵植物的分布和环境数据为基础,应用除趋势对应分析、典范对应分析和回归分析方法,探讨了我国境内入侵植物区系组成、地理分布格局及其影响因素。主要结果如下:(1)我国74个地区共有282种外来入侵种,出现频率相对较高的外来入侵种是小飞蓬(Conyza canadensis)、刺苋(Amaranthus spinosus)、一年蓬(Erigeron annuus)、空心莲子草(Alternathera philoxeroides)、土荆芥(Chenopodium ambrosioides)、圆叶牵牛(Pharbitis purpurea)、曼陀罗(Datura stramonium)、皱果苋(Amaranthus viridis)、裂叶牵牛(Pharbitis nil)、反枝苋(Amaranthus retroflexus)、三叶鬼针草(Bidens pilosa)、凤眼莲(Eichhornia crassipes)等;(2)菊科(Compositae,67,种数)、禾本科(Gramineae,32)、豆科(Leguminosae,29)、苋科(Amaranthaceae,23)、旋花科(Convolvulaceae,13)是我国境内含入侵种最丰富的5个科,共计有164种,占我国入侵植物总数的58.16%;(3)我国外来入侵植物主要源自于热带美洲、北美洲、欧洲、地中海-西亚和中亚、非洲和南亚;(4)外来入侵植物多样性在我国的区域分异明显,热带-南亚热带、中(北)亚热带和温带三大区域的入侵种组成有较大差异:马缨丹(Lantana camara)、含羞草(Mimosapudica)、胜红蓟(Ageratum conyzoides)、刺苋、小飞蓬、飞扬草(Euphorbia hirta)、五爪金龙(Ipomoea cairica)、空心莲子草、三叶鬼针草和金腰箭(Synedrella nodiflora)是热带-南亚热带区域中出现频率最高的前10种入侵植物;中亚热带和北亚热带区域出现频率最高的入侵种分别是一年蓬、小飞蓬、刺苋、土荆芥、北美独行菜(Lepidium virginicum)、美洲商陆(Phytolacca americana)、牛筋草(Eleusine indica)、紫茉莉(Mirabilis jalapa)、空心莲子草和三叶鬼针草;温带区域出现频率最高的是反枝苋、小飞蓬、圆叶牵牛、一年蓬、野西瓜苗(Hibiscus trionum)、杂配藜(Chenopodium hybridum)、苦苣菜(Sonchus oleraceus)、野燕麦(Avena fatua)、曼陀罗和皱果苋;(5)年降雨量、年均温度、年极端低温、无霜期和年均积温是影响我国外来入侵种空间分布格局的主要气象因素,年极端高温和年日照时数的影响相对较小;人口密度和交通密度对入侵种的地理分布也均有很大的影响;(6)随着年均温度、无霜期、人口密度、交通密度、年极端低温、年均降雨量和年积温的增加,外来入侵植物的种数呈线性增加,随着纬度的增加,种数则呈线性递减,种数与这8个环境因素间的关系达到极显著的水平;(7)不同地理来源的外来入侵种在我国的分布主要受纬度、年降雨量、年均无霜期、年均温度、交通密度、年极端低温和年均积温的影响。由于外来入侵种在我国分布呈现明显的区域分化,因此,应用建立具有区域特点的外来植物入侵风险评估系统。