Computer assisted floristic similarity analysis

A program for polythetic numerical evaluation of phytosociological material is described. Using Sörensen's coefficient of floristic similarity it computes the homogeneity of subjectively chosen sets of relevés, the affinity of each constituent relevé to the set as well as the similarity between any pair of sets. It is also able to plot a dendrogram of the hierarchic system obtained by agglomerating individual relevés into complex groupings. The program is suitable for processing phytosociological data arranged in any conventional table.     

Arranging phytosociological tables by species-relevé groups

Abstract. A newmethod of arranging phytosociological tables by species-relevé groups (blocks) on the basis of the density of rows and columns (relative species frequency and relative species number) is presented. Each block fulfils a given minimum criterion regarding its density. With a density threshold of e.g. 50 %, blocks are formed with only those species that are present in at least 50 % of the block's relevés, while at the same time the block's relevés comprise at least 50 % of the block's species. The procedure starts with the complete table and iteratively masks species and relevés with the smallest densities. This is performed step by step with species and relevés and continues until the given density threshold for all species and relevés is exceeded. Without any further parameters other than the minimum density, species-relevé groups of gradually decreasing size are formed. Data processing is performed with a computer program (ESPRESSO). The main application of the method is found in an effective pre-sorting of relevé data. The blocks formed can be arranged in the final table as desired.     

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.     

TURBOVEG,a comprehensive data base management system for vegetation data

Abstract. The computer software package TURBOVEG (for Microsoft® Windows®) was developed in The Netherlands for the processing of phytosociological data. This package comprises an easy‐to‐use data base management system. The data bank to be managed can be divided into several data bases which may consist of up to 100 000 relevés each. The program provides methods for input, import, selection, and export of relevés. In 1994, TURBOVEG was accepted as the standard computer package for the European Vegetation Survey. Currently it has been installed in more than 25 countries throughout Europe and overseas.     

Formalized reproduction of an expert‐based phytosociological classification: A case study of subalpine tall‐forb vegetation

Abstract. Delimitation of vegetation units in phytosociology is traditionally based on expert knowledge. Applications of expert‐based classifications are often inconsistent because criteria for assigning relevés to vegetation units are seldom given explicitly. Still, there is, e.g. in nature conservation, an increasing need for a consistent application of vegetation classification using computer expert systems for unit identification. We propose a procedure for formalized reproduction of an expert‐based vegetation classification, which is applicable to large phytosociological data sets. This procedure combines Bruelheide's Cocktail method with a similarity‐based assignment of relevés to constancy columns of a vegetation table. As a test of this method we attempt to reproduce the expert‐based phytosociological classification of subalpine tall‐forb vegetation of the Czech Republic which has been made by combination of expert judgement and stepwise numerical classification of 718 relevés by TWINSPAN. Applying the Cocktail method to a geographically stratified data set of 21794 relevés of all Czech vegetation types, we defined groups of species with the statistical tendency of joint occurrences in vegetation. Combinations of 12 of these species groups by logical operators AND, OR and AND NOT yielded formal definitions of 14 of 16 associations which had been accepted in the expert‐based classification. Application of these formal definitions to the original data set of 718 relevés resulted in an assignment of 376 relevés to the associations. This assignment agreed well with the original expert‐based classification. Relevés that remained un‐assigned because they had not met the requirements of any of the formal definitions, were subsequently assigned to the associations by calculating similarity to relevé groups that had already been assigned to the associations. A new index, based on frequency and fidelity, was proposed for calculating similarity. The agreement with the expert‐based classification achieved by the formal definitions was still improved after applying the similarity‐based assignment. Results indicate that the expert‐based classification can be successfully formalized and converted into a computer expert system.     

Phytosociological data give biased estimates of species richness

Abstract. Large phytosociological data sets of three types of grassland and three types of forest vegetation from the Czech Republic were analysed with a focus on plot size used in phytosociological sampling and on the species‐area relationship. The data sets included 12975 relevés, sampled by different authors in different parts of the country between 1922 and 1999. It was shown that in the grassland data sets, the relevés sampled before the 1960s tended to have a larger plot size than the relevés made later on. No temporal variation in plot sizes used was detected in forest relevés. Species‐area curves fitted to the data showed unnatural shapes, with levelling‐off or even decrease in plot sizes higher than average. This distortion is explained by the subjective, preferential method of field sampling used in phytosociology. When making relevés in species‐poor vegetation, researchers probably tend to use larger plots in order to include more species. The reason for this may be that a higher number of species gives a higher probability of including presumed diagnostic species, so that the relevé can be more easily classified in the Braun‐Blanquet classification system. This attitude of phytosociologists has at least two consequences: (1) in phytosociological data bases species‐poor vegetation types are underrepresented or relevés are artificially biased towards higher species richness; (2) the suitability of phytosociological data for species richness estimation is severely limited.     

Common data standards for recording relevés in field survey for vegetation classification

Abstract. In the framework of the European Vegetation Survey common data standards are proposed for recording phytosociological relevés for syntaxonomical classification. The authors wish to establish the notion that common data standards for recording phytosociological data can only be advantageous for advancing the credibility and application of vegetation science, and may stimulate other projects.     

Plot sizes used for phytosociological sampling of European vegetation

Abstract. In European phytosociology, variable plot sizes are traditionally used for sampling different vegetation types. This practice may generate problems in current vegetation or habitat survey projects based on large data sets, which include relevés made by many authors at different times. In order to determine the extent of variation in plot sizes used in European phytosociology, we collected a data set of 41 174 relevés with an indication of plot size, published in six major European journals focusing on phytosociology from 1970 to 2000. As an additional data set, we took 27 365 relevés from the Czech National Phytosociological Database. From each data set, we calculated basic statistical figures for plot sizes used to sample vegetation of various phytosociological classes. The results show that in Europe the traditionally used size of vegetation plots is roughly proportional to vegetation height; however, there is a large variation in plot size, both within and among vegetation classes. The effect of variable plot sizes on vegetation analysis and classification is not sufficiently known, but use of standardized plot sizes would be desirable in future projects of vegetation or habitat survey. Based on our analysis, we suggest four plot sizes as possible standards. They are 4 m² for sampling aquatic vegetation and low‐grown herbaceous vegetation, 16 m² for most grassland, heathland and other herbaceous or low‐scrub vegetation types, 50 m² for scrub, and 200 m² for woodlands. It has been pointed out that in some situations, sampling in either small or large plots may result in assignment of relevés to different phytosociological classes or habitat types. Therefore defining vegetation and habitat types as scale‐dependent concepts is needed.     

A phytosociological classification of Swiss mire vegetation

The mapping and monitoring of Swiss mires has so far relied on a classification system based on expert judgement, which was not supported by a quantitative vegetation analysis and which did not include all wetland vegetation types described in the country. Based on a spatially representative sample of 17,608 relevés from 112 Swiss mires, we address the following questions: (1) How abundant are wetland vegetation types (phytosociological alliances) in Swiss mires? (2) How are they distributed across the country––is there a regional pattern? (3) How clearly are they separated from each other? (4) How clear and reliable is their ecological interpretation? Using published wetland vegetation relevés and lists of diagnostic species for phytosociological units (associations and alliances) established by experts, we developed a numerical method for assigning relevés to units through the calculation of similarity indices. We applied this method to our sample of 17,608 relevés and estimated the total area covered by each vegetation type in Switzerland. We found that vegetation types not included in previous mapping were either rare in Switzerland (partly due to mire drainage) or poorly distinguished from other vegetation units. In an ordination, the Swiss mire vegetation formed a triangular gradient system with the Sphagnion medii, the Caricion davallianae and the Phragmition australis as extreme types. Phytosociological alliances were clearly separated in a subset of 2,265 relevés, which had a strong similarity to one particular association, but poorly separated across all relevés, of which many could not be unequivocally assigned to one association. However, ecological gradients were reflected equally well by the vegetation types in either case. Overall, phytosociological alliances distinguished until now proved suitable schemes to describe and interpret vegetation gradients. Nevertheless, we see the urgent need to establish a data base of Swiss wetland relevés for a more reliable definition of some vegetation units.     

A Phytosociological Survey of the Chionophilous Communities of Western North America. Part I: Temperate and Mediterranean Associations

Through tabular and average linkage cluster analyses, 872 phytosociological relevés, including 491 obtained from the literature and 381 of our own relevés obtained in the field, were ordered and classified. Based on these relevés, we then described and typified the associations, alliances, orders, subclasses, and classes defining the chionophilous communities of the boreal, temperate and Mediterranean climates of western North America. Diagnostic tables, ordination, clustering, and climatic, edaphic, and biogeographical data were used to establish floristic affinities among these syntaxa and interpret their distributions. Syntaxa were characterized by their floristic composition, physiognomy and biogeographical distribution, along with their position on the snow gradient. Finally, we ascribed the communities growing in temperate and Mediterranean climates to the new class Hieracio gracilis-Juncetea drummondii, including 3 subclasses, 6 orders, 12 alliances and 34 associations.     

Numerical reproduction of traditional classifications and automatic vegetation identification

Questions: Is it possible to develop an expert system to provide reliable automatic identifications of plant communities at the precision level of phytosociological associations? How can unreliable expert‐based knowledge be discarded before applying supervised classification methods? Material: We used 3677 relevés from Catalonia (Spain), belonging to eight orders of terrestrial vegetation. These relevés were classified by experts into 222 low‐level units (associations or sub‐associations). Methods: We reproduced low‐level, expert‐defined vegetation units as independent fuzzy clusters using the Possibilistic C‐means algorithm. Those relevés detected as transitional between vegetation types were excluded in order to maximize the number of units numerically reproduced. Cluster centroids were then considered static and used to perform supervised classifications of vegetation data. Finally, we evaluated the classifier's ability to correctly identify the unit of both typical (i.e. training) and transitional relevés. Results: Only 166 out of 222 (75%) of the original units could be numerically reproduced. Almost all the unrecognized units were sub‐associations. Among the original relevés, 61% were deemed transitional or untypical. Typical relevés were correctly identified 95% of the time, while the efficiency of the classifier for transitional data was only 64%. However, if the second classifier's choice was also considered, the rate of correct classification for transitional relevés was 80%. Conclusions: Our approach stresses the transitional nature of relevé data obtained from vegetation databases. Relevé selection is justified in order to adequately represent the vegetation concepts associated with expert‐defined units.     

Vegetation and environmental factors during primary succession on glacier forelands: Some outlines from the Italian Alps

ABSTRACT

Relationships between plant communities and the physical environment during primary succession on recently deglaciated glacier forelands were studied in 3 areas of the Italian Alps. The aim of the research was to relate traditional phytosociological data with environmental variables. Twenty-eight phytosociological relevés were performed, each associated with twenty-six environmental variables; quantitative parameters of richness and diversity were also calculated. Species/relevés, environmental variables/relevés and species/environmental variables matrices were analyzed by cluster analysis, PCA and Spearman correlation coefficient. Three main stages of succession were identified by floristic composition and confirmed by environmental parameter evaluation. A complex of environmental variables seems to be closely correlated with terrain age and richness/diversity parameters, even though diversity decreases in late successional stages. The phytosociological significance of species is in accordance with their position in the context of succession.     

Bayesian classification of vegetation types with Gaussian mixture density fitting to indicator values

Question: Is it possible to mathematically classify relevés into vegetation types on the basis of their average indicator values, including the uncertainty of the classification? Location: The Netherlands. Method: A large relevé database was used to develop a method for predicting vegetation types based on indicator values. First, each relevé was classified into a phytosociological association on the basis of its species composition. Additionally, mean indicator values for moisture, nutrients and acidity were computed for each relevé. Thus, the position of each classified relevé was obtained in a three‐dimensional space of indicator values. Fitting the data to so called Gaussian Mixture Models yielded densities of associations as a function of indicator values. Finally, these density functions were used to predict the Bayesian occurrence probabilities of associations for known indicator values. Validation of predictions was performed by using a randomly chosen half of the database for the calibration of densities and the other half for the validation of predicted associations. Results and Conclusions: With indicator values, most reléves were classified correctly into vegetation types at the association level. This was shown using confusion matrices that relate (1) the number of relevés classified into associations based on species composition to (2) those based on indicator values. Misclassified relevés belonged to ecologically similar associations. The method seems very suitable for predictive vegetation models.     

A simple method for estimating homotoneity of sets of phytosociological relevés

The homogeneity of sets of phytosociological relevés or syntaxa—the homotoneity—is tested by means of a homotoneity-coefficient. This coefficient consists of the basic homotoneity-coefficient expressing the proportion of highly constant species (61–100%) in the species composition of the average relevé and the correcting factor which is proportional to the difference of species number between the richest and poorest relevé. Successive analysis of heterotoneity of sets of relevés for detecting sources of heterotoneity is proposed.     

Some notes on estimation of the basic homoteneity-coefficient of sets of phytosociological relevés

The formula for calculation of the basic homotoneity-coefficient of sets of phytosociological relevés does not give adequate values for sets of 4 or 3 relevés. Therefore an empirical correction procedure is proposed for the calculation of this coefficient for such small sets of relevés. For sets of 2 relevés the calculation of the basic homotoneity-coefficient gives values equal toSørensen’s coefficient of floristic similarity. A simplification of calculation of the basic homotoneity-coefficient for sets of more than 20 relevés is proposed.     

Towards unification of national vegetation classifications: A comparison of two methods for analysis of large data sets

Abstract. In European phytosociology, national classifications of corresponding vegetation types show considerable differences even between neighbouring countries. Therefore, the European Vegetation Survey project urgently needs numerical classification methods for large data sets that are able to produce compatible classifications using data sets from different countries. We tested the ability of two methods, TWINSPAN and COCKTAIL, to produce similar classifications of wet meadows (Calthion, incl. Filipendulenion) for Germany (7909 relevés) and the Czech Republic (1287 relevés) in this respect. In TWINSPAN, the indicator ordination option was used for classification of two national data sets, and the extracted assignment criteria (indicator species) were applied crosswise from one to the other national data set. Although the data sets presumably contained similar community types, TWINSPAN revealed almost no correspondence between the groups derived from the proper classification of the national data set and the groups defined by the assignment criteria taken from the other national data set. The reason is probably the difference in structure between the national data sets, which is a typical, but hardly avoidable, feature of any pair of phytosociological data sets. As a result, the first axis of the correspondence analysis, and consequently the first TWINSPAN division, are associated with different environmental gradients; the difference in the first division is transferred and multiplied further down the hierarchy. COCKTAIL is a method which produces relevé groups on the basis of statistically formed species groups. The user determines the starting points for the formation of species groups, and groups already found in one data set can be tested for existence in the other data set. The correspondence between the national classifications produced by COCKTAIL was fairly good. For some relevé groups, the lack of correspondence to groups in the other national data set could be explained by the absence of the corresponding vegetation types in one of the countries, rather than by methodological problems.     

Phytosociological studies at malham tarn moss and fen,Yorkshire, England

Summary During a field course the vegetation of the extensive mire complex on the west side of Malham Tarn was examined. 84 relevés were collected, with 210 taxa in total. This data set has been ‘structured’ by classical phytosociological techniques. It is suggested that it approaches the maximum size of data-set which can be handled in this way, especially if the data are not all collected by one person. Ordination of the quadrats was carried out but gave little insight into the data despite the use of non-centred as well as centred principal components analysis. Numerical classification of the quadrats using minimumvariance cluster analysis was shown to produce a structure interpretable in ecological terms. A classification of the taxa was carried out by the same method and a ‘rearranged’ table was drawn up using the results of the two classifications. A relocation technique was applied at an appropriate cluster level but little was felt to be gained from this. The use of ‘two-way’ minimum-variance cluster analysis for the rapid production of re-arranged tables is recommended for large data-sets. In addition the vegetational units recognised in the data are described and discussed. The authors wish to thank Miss D. R. Clowes, Mr. P. Gladders, Mr. A. R. Hall, Mr. R. N. Lentell, and Mr. J. E. Young for assistance in the collection of the data, and Mrs. M. E. Pettit and Mrs. S. Peglar for assistance in the data processing.     

Multi-scaled pattern analysis: An example with savanna vegetation and a proposal for a sampling design

A detailed pattern analysis has been undertaken in a savanna vegetation, at several scales, using statistical and other data analytical methods. Monospecific patterns were studied at 11 different scales: five scales within the relevés and six starting with the relevé scale. The examination of the connection between the monospecific patterns and the results of multivariate analyses reveals the phytosociological properties of these latter methods. Conclusions about a future design are drawn.     

Validity of Ellenberg indicator values judged from physico‐chemical field measurements

Abstract. The relationship between mean Ellenberg indicator values (IV) per vegetation relevé and environmental parameters measured in the field usually shows a large variation. We tested the hypothesis that this variation is caused by bias dependent on the phytosociological class. For this purpose we collected data containing vegetation relevés and measured soil pH (3631 records) or mean spring groundwater level (MSL, 1600 records). The relevés were assigned to vegetation types by an automated procedure. Regression of the mean indicator values for acidity on soil pH and the mean indicator values for moisture on MSL gave percentages explained variance similar to values that were reported earlier in literature. When the phytosociological class was added as an explanatory factor the explained variance increased considerably. Regression lines per vegetation type were estimated, many of which were significantly different from each other. In most cases the intercepts were different, but in some cases their slopes differed as well. The results show that Ellenberg indicator values for acidity and moisture appear to be biased towards the values that experts expect for the various phytosociological classes. On the basis of the results, we advise to use Ellenberg IVs only for comparison within the same vegetation type.