Influences of transformation of cover values on classification and ordination of lake vegetation

Summary Numerical ordination (Program ORDINA) and classification (Program TABORD) have been applied to vegetation data from a lake in south Sweden.Full percentage values and different transformations of the estimated percented cover scale have been tested on relevés with nymphaeids (+ elodeids) and on relevés containing obly helophytes. The used scales have been: percentage (P), Hult-Sernander-Du Rietz (HSD), Log (%+1) (LP), 1+ log% (L), 100+ % (HP) and Presence/Absence (P/A). The main aim has been to find if there is an optimal transformation regarding both quantitative and qualitative information in vegetation data.In the classification of helophytes a dataset with 87 relevés and 20 species have been used applying P-and L-scales and P/A. The similarity between the different scales has been compared in relation to common relevés between every two corresponding clusters. L and P/A give very similar results, more similar than L and P or PA and P. It is also interesting that the result with P-scale is more similar to L than to P/A. The P-scale neglects with the species with a low cover value, whilst the L-scale takes notice of both quantity and quality.In the classification of 90 nymphaeid relevés containing only 6 species P, HSD, L, HP and P/A were applied. The L-scale (and partly PH-scale) gave a result similar to the most quantitative P-and HSD-scales. P/A-values gave a very deviating result. In the ordination of helophytes only 38 relevés with 18 species, taken along a transcect, were used and P, P/A and 4 different transformations were applied. The similarity between order of relevés in the graphs and real order of relevés along the transect was used as an objective test of the effectiveness of the scale applied. The P-scale gave a bad result, whilst P/A gave the best result. The intermediate scales L and HP gave acceptable results.In the ordination of nymphaeids (+ elodeids) 90 relevés, where only pattern was studied, the L-scale gave the best result most similar to P-and HSD, but applying the two extremes, P-scale and P/A, resulted in large reduction of information.In the submitted ordinations and classifications the applied L-scale (and HP-scale) always gave ecologically interpretable results, but the extreme transformation were less reliable.This work has been supported by grants from the University of Lund, for which I am duty grateful.Nomenclature follows Lid (1974).I am grateful to Professor Nils Malmer, head of the Department of Plant Ecology, Lund, Sweden, Dr. Eddy van der Maarel, University of Nijmegen, Holland, and my colleague Fil. Kand. Stefan Persson for valuable advice and discussions. I also thank my wife Fil. Kand. Eva Waldemarsson Jensén, Institute of Ecological Botany, Uppsala, for valuable discussions, Mr. Tommy Olsson for valuable technical advice, Dr. R.S. Clymo for advice with DIVINF and PCA and correction of the language, Mrs. Mimmi Varga for drawing the figures and Mrs. Brita Billstein for typewriting the text and the tables.     

Measurement of the predictive value of species lists for species cover in phytosociological samples

The method known as Analysis of Concentration (AOC) is proposed as a tool to measure the predictivity of binary data for cover data. The application of AOC to structured tables of oak forests of Central Italy has proved that binary data are more predictive for cover than cover for binary data. The ordinations produced by AOC with binary and cover data are very similar and interpretable with similar results.     

An application of ordination to the identification of forest types

Summary The problems of allocating new vegetation stands to an existing classification are outlined. As one solution, the vegetation samples from an area may be ordinated by reciprocal averaging and classified by dividing the ordination into community-types. The ordination scores for a short list of species present in a new sample may then be averaged to locate that sample on the ordination axes and in one of the community-types. The method is tested by comparing estimates from incomplete species lists with that from a complete list of species in an forest stand in southern Ghana.We gratefully acknowledge the assistance of Mr. M.O. Hill in the correct formulation of the coordinate estimation procedure.     

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。     

On the manipulation and editing of phytosociological and ecological data

Editing and other manipulations of phytosociological data are considered parts of a more comprehensive data management program. The topic is reviewed against the background of an increasing number of presentations in Vegetatio. It is observed that the newer editing programs do not add anything new to the already existing battery of programs. Yet, there is a need for further discussions of some risks in data manipulations, notably a priori deletion of relevés and species transformation of field scores, and incorporation of suitable devices in the packages available. Also, the evaluation of classification results and the allocation of new material to existing classification systems need more attention. So do the problems concerning the production of structured phytosociological tables, as outcomes of multivariate data treatments.     

Classification and ordination in the Indian Peaks area,Colorado Rocky Mountains

Summary A mid-latitude, Northern Hemisphere alpine vegetation in the Colorado Rocky Mountains was suitable for analysis by syntaxonemie and numerical methods, which interpreted the Braun-Bianquet association data, distributed by habitat and vegetation dominance types, correspondingly. Classification and ordination yielded complementary, interpretable results, which combined were more informative than results of either technique alone. Syntaxonomic results can faeilitate the interpretation of numerical results; the syntaxonomic relationships can be clarified by the results of numerical analysis.Alliances and orders of the Braun-Blanquet hierarchy, and their diagnostic taxa groups were derived by numerical methods from an association/taxa matrix. On the basis of this matrix, numerical methods demonstrated some of the environmental gradient complexes controlling the compositional variation. The compositional distinctiveness and uniformity of orders and alliances parallel environmental distictiveness and uniformity.The following attributes of the sampled vegetation and environment were probably responsible for the successful combination of syntaxonomic and numerical results: 1. The sampled area as a geographically limited universe, characterized by relative environmental, biotic, and historical distinctiveness and uniformity, 2. The wide range, high diversity, and clear denfinition of habitat and vegetation dominance types. Because it effectively summarizes and simplifies field data, syntaxonomy can play an important role in building local vegetatio models.Most of the figures in this paper are from a book version of a University of Colorado, Department of Environmental, Population, and Organismic Biology, Ph. D. thesis which was produced at the Institute of Arctic and Alpine Research. I would like to thank Dr. P.J. Webber, the thesis advisor, for his support, for suggesting the numerical methods, and for computer programs which were written by W.F. Reid. Vicki Dow, Marilyn Joel, and Karen Sproul drafted the majority of figures. I am grateful to Gwen Archer for editorial help.     

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     

Multivariate approach to the classification and ordination of the forest ecosystem of Nandiar valley western Himalayas

QuestionsDoes the vegetation composition of the forests of Nandiar Valley correlate with climatic, topographic and edaphic variables? Is it possible to identify plant communities through indicator species in relation to environmental gradients? Can this approach of classification and ordination will be helpful for conservation planning?LocationForests of Nandiar Valley, Moist temperate Western Himalayas Pakistan.MethodsEighty stands were selected for quantitative and qualitative characteristic of vegetation between an elevations of 525–3817 m. Species composition was recorded by using 400 m long transects. GPS, climatic, edaphic and topographic data were recorded for each sampling site. The relationship between habitat types, species composition and distribution along with climatic, edaphic and topographic variables were analyzed using TWINSPAN, Cluster analysis and DCA ordination.ResultsSum 325 vascular plants species belonging to 97 families were recorded. Diversity index and species richness was maximum in the moist temperate zone. Classification and ordination showed that the variance in species data was 7.07. Two-ways indicator species analysis classified the vegetation into eight plant communities. Indicator species analysis revealed that slope aspect, wind speed, temperature, dew point, wet bulb, pH, organic matter and phosphorous were the strongest parameters (p ≤ 0.05) determining plant community composition and indicator species in each habitat. The results also show the strength of the environment – species relationship using Monte Carlo procedures. DCA ordination grouped different species having similar habitat and habitats having common species.ConclusionsThe multivariate analysis of the vegetation along with environmental variables of Nandiar valley confirmed the indicators of each sort of vegetation communities/microclimatic zones which could further be used in conservation planning and management not only in studied area but also in the adjacent regions as well as in the areas exhibit similar sort of climatic, edaphic and topographic conditions.     

Classification of lakes in Southern Sweden on the basis of their macrophyte composition by means of multivariate methods

Summary Methods developed by Jensén (1977, 1978) have been used to typify 50 lakes in Scania, S Sweden, according to their macrophyte composition. The macrophytic vegetation has been treated numerically both by classification programs (DIVINF, TABORD) and ordination programs (Reciprocal averaging, PCA). Characteristic cover (%), relevé frequency (%) and transect frequency (%) for each species in each lake have been used in the numerical treatment. The values of the attributes have been transformed to a logarithmic scale: 100 (1+log Cover %). In the classification the species have been divided into two life forms (helophytes = H, nymphaeids = N) and a life-form group (elodeids, lemnids and Isoetids = ELI). Classifications have resulted in ten helophyte lake types, eleven ELI lake types and 6 nymphaeid lake types (fusion limit of similarity ratio = 0.80) and 3 helophyte, 5 ELI and 4 nymphaeid groups of lake types (fusion limit 0.30).The three helophyte groups were characterized by Carex-Equisetum, Seirpus lacustris and Phragmites communis respectively. The ELI groups were characterized by (i) the almost complete lack of ELI, (ii) sparse elodeids, (iii) isoetids, (iv) lemnids + elodeids. The nymphaeid groups were characterized by (i) Potamogeton natans (scattered) (ii) dense co-dominance of Nuphar luteum, Nymphaea alba and Potamogeton natans, (iii) Nuphar luteum (+ Polygonum amphibium) and (iv) lack of nymphaeids.In every lake there is one of the 10 H types, one of the 6 N types and one of the 11 ELI types present the combinations generally varying from lake to lake. A given H type is often found together with a given ELI type while a given N type occurs less often with a given ELI type or a given H type (fusion limit 0.80). At fusion limit 0.30 the combinations of a certain H, ELI and N type occur more regularly. The results show that lakes must be classified on the basis of the two life-forms (H and N) and the life-form group (ELI) to indicate the true macrophyte composition of a given lake as compared with other lakes.Nomenclature follows Lid (1974); Juncus bulbosus f. fluitans is shortened to Juncus fluitans.I am grateful to Professor Nils Malmer, head of the Department of Plant Ecology, Lund, Sweden, Dr. Eddy van der Maarel, University of Nijmegen, Holland, Professor Hans Mathiesen, University of Aarhus, Denmark, and my colleague Fil. Kand. Stefan Persson for valuable advice and discussions. I also thank my wife Fil. Kand. Eva Waldemarson Jensén, Institute of Ecological Botany, Uppsala, for valuable discussions, Dr. R.S. Clymo for advice with ordination, Mr Åke Rühling for valuable technical advice, Mr. Henry Letocha for correction of the language, Mrs. Mimmi Varga for drawing the figures and Mrs. Brita Billstein for typewriting the text and the tables.This work has been suported by grants from the University of Lund, for which I am duly grateful.     

Performance of four ordination techniques assuming three different non-linear species response models

Summary The performances of four ordination techniques (reciprocal averaging, parametric mapping, gaussian ordination and non-metric multidimensional scaling) are evaluated using artificial data based on three vegetation models: the gaussian response curve, -function curves, and an ecological response model. No technique performs well with the artificial data not based on a gaussian model. Non-metric multidimensional scaling seemed marginally better than other techniques. Some of the implications of this failure are discussed.     

The conceptual basis for a new classification of the coccidia

At the joint meeting of the 8th International Coccidiosis Conference and the Annual Scientific Meeting of the Australian Society for Parasitology in Palm Cove, Australia, in July 2001, a Controversial Roundtable was held on 'New classification of coccidia'. The aim of this Roundtable was to stimulate and encourage discussion and debate on current classification schemes for the group of parasitic protozoa known as the eimeriid coccidia. In the past, such classifications have been based only on phenotypic characters such as morphology, ultrastructure, life cycles, and host specificity. However, over the past 10-15 years, molecular phylogenetic studies on taxa of the eimeriid coccidia have revealed that several of the families, subfamilies, and genera that have been erected based on non-molecular characters are paraphyletic. Therefore, this Roundtable was an important forum for initial discussions on how a new and more comprehensive classification of the eimeriid coccidia, which takes into consideration both phenotypic and molecular characters, can be devised. The stimulus came from invited speakers who gave introductions into selected areas of taxonomy and classification. Following these introductions, a more general discussion with the audience addressed potential steps that may be taken in future work. This review is the immediate outcome of the Roundtable. It describes advantages and disadvantages of the use of phenotypic or molecular characters as the base for taxonomic schemes for eimeriid coccidia. It gives specific examples for drawbacks of current classifications based only on phenotypic characters as well as potential pitfalls associated with the use of only molecular phylogenies. It addresses current controversies as well as rules of taxonomy and nomenclature relevant for the eimeriid coccidia. Finally, it recommends the establishment of an international group of scientists to meet on a regular basis, stimulate further discussions, and give direction on how the final goal, i.e. a proposal for a revised, and widely accepted, classification of the eimeriid coccidia, may be achieved.     

Clusla: A computer program for the clustering of large phytosociological data sets

Summary CLUSLA, a computer program for the clustering of very large phytosociological data sets is described. It is an elaboration of Janssen's (1975) simple procedure. The essence of the program is the creation of clusters, each starting with one relevé, as the relevés are entered in the program. Each new relevé that is sufficiently distinct from already existing clusters is considered a new cluster. The fusion criterion is the attainment of a certain level of (dis-) similarity between relevé and cluster. Bray and Curtis' dissimilarity measure with presence-absence data was used.The program, written in FORTRAN for an IBM 370–158 system, can deal with practically unlimited numbers of relevés, provided the product of the number of primary clusters and the number of species does not exceed 140.000. We adopted maxima of 100 and 1400 respectively.After the primary clustering round a reallocation is performed. Then a simple table is printed with information on the significance of occurrence of species in clusters according to a chi-square approach. The primary clusters can be treated again with a higher fusion threshold; or approached with more elaborate methods, in our case particularly the TABORD program.The program is demonstrated with a collection of 6072 relevés with 889 species of salt marsh vegetation from the Working-Group for Data-Processing.Contribution from the Working Group for Data-Processing in Phytosociology, International Society for Vegetation Science. Nomenclature follows the Trieste system, which will be published later.The authors are very grateful to Drs. Jan Janssen, Mike Dale, László Orlóci and Mike Austin for their comments on drafts of the program, and to Wil Kortekaas for her help in the interpretation of the tables.     

Vegetation–environment relationships and classification of the seasonal savannas in Venezuela

The seasonal savannas dominated by the C₄ grasses of the genus Trachypogon, are widespread in northern South America. In Venezuela, they extend from the central lowland Llanos to intermediate elevations in the Coastal and Andean Mountains and to the Guiana Plateau (Gran Sabana) in the south. This study aims to classify these savannas and to understand the environmental factors that determine their composition and structure. Thirty-seven sites were sampled, plant cover and density were measured in 376 one square meter quadrats and the importance value index (IVI) was calculated. Climate data were obtained from climatological stations and soil properties were analyzed. The results were classified by clustering and TWINSPAN. Floristic and environmental data were ordered with the canonical correspondence analysis (CCA).Trachypogon savannas are heterogeneous, both floristically and environmentally. An altitudinal gradient of 2000 m separates the intermediate elevation Coastal Mountains (Type I) and the Guiana savannas (Type II) from the lowland Llanos. In the lowlands, sparsely covered and treeless communities on extremely oligotrophic and sandy soils (Type IV) differ structurally and floristically from woody savannas (Type III). The floristics and structure of the savannas respond directly or indirectly to elevation and water and nutrient availability. These responses were evidenced by: (a) floristic composition, as Neotropical lowland savanna species merged with those of the Andean sub-páramo in Type I savannas or with those from the Guianan flora in Type II savannas. (b) Species richness, which ranged from an average of 13.8 per site in sandy Type IV savannas to 38.9 per site in Type I intermediate elevation savannas. (c) Community physiognomy, which changes from an homogeneous herbaceous matrix with dispersed trees in Type III savannas to a shrubby Type I savannas to “treeless” Types II and IV savannas. (d) Plant cover which varied from 93.8% in the fertile Type I savannas to around 80% in the sandy oligotrophic savannas of Types II and IV. Each savanna type is related to one of the major geomorphological regions of Venezuela.     

DCCA排序轴分类及其在关帝山八水沟植物群落生态梯度分析中的应用

首次在ＤＣＣＡ排序的基础上使用排序轴分类法（ＯＡＣ）,将其发展为一个新的典范分类方法,并应用这种方法对山西关帝山八水沟的植物群落进行了数量分类,共划分出５类,效果较好。方差分析与多重比较表明,环境与群落结构因子在不同群落之间存在较为显著的差异,表明ＤＣＣＡ排序轴分类法能较好地反映群落与环境的变异。因为ＤＣＣＡ排序轴分类同时结合了植被因子与环境因子,所以它能较好地表达植物群落的环境梯度和结构梯度,反