Species ordering on a variance criterion

Summary A technique for ordering, to identify diagnostic species, based on variance ratios has been described. The method was illustrated with river terrace data.The author would like to thank Dr. László Orlóci for permission to use the vegetation data employed in the illustration of the algorithm. This work was supported by a grant from the National Research Council of Canada.     

A heuristic test for homogeneity in species populations

Summary This paper elaborates on the notion of homogeneity in plant populations and its quantification. It describes a method for testing homogeneity without the need to make assumptions about generalized distributions. The implementation of the method is illustrated through actual numerical examples.This paper presents results from a study of plant populations for which a National Research Council of Canade grant has been received (L. Orlóci).     

A resemblance function based on probability: Applications to field and simulated data

A resemblance function (COCHIS) based on the probability of species association and correlation is proposed. It is a development of the underlying idea of association analysis and can serve to produce similarity matrices for polythetic classifications and ordinations. Examples are given utilizing field and simulated data.The work has been supported by the Italian Ministry of Education. We would like to thank the Profs. D W. Goodall, E. van der Maarel and I. Orlóci for comments.     

Towards the analysis of vegetation succession

Attention is drawn to canonical analysis as a plausible model for analyzing vegetation succession. An assessment of the opportunities afforded by canonical analysis for this purpose is then made by reference to two applications of the method. The applications deal with characteristics of hydroseral processes and with the dynamic status of an area of lowland tropical rain forest. On the basis of these and other studies the conclusion is drawn that canonical analysis could contribute usefully in efforts to place the study of dynamic ecosystem processes on a more analytic footing.This work was supported by a Natural Sciences and Engineering Research Council award to L. Orlóci. It is a pleasure to acknowledge my indebtedness both to Dr. Orlóci for his support and encouragement and to the Department of Plant Sciences at the University of Western Ontario for hospitality and help. Appreciation is expressed also to Dr. John Ogden, Research School of Pacific Studies, The Australian National University, Canberra for kindly placing his rain forest data at my disposal and for his invaluable help in interpreting the results of analyses of these data.     

Species dispersion profiles of anthropogenic grasslands in the Italian Eastern Pre-Alps

A method is proposed to analyse the dispersion profiles of species in classes of environmental variables, based on the decomposition of the expected frequencies in contingency tables with many interacting species. The method has been applied to data of dominant or very frequent graminoid species in grasslands of the Natisone Valley (Friuli, Italy). It allowed to make predictions by removing the random component of variation.Nomenclature follows: P. Zangheri (1976). Flora Italica, CEDAM, Padua.The authors were recipients of an Italian CNR grant (E. Feoli) and a Canadian NSERC grant (L. Orlóci) during tenure of this project. The results are in partial fulfillment of a commitment to the Centro Regionale per la Sperimentazione Agraria per il Friuli-Venezia Giulia.     

Numerical studies of compositional gradients in oreophilous vegetation (northern Apennines,Italy)

Summary A numerical study of a set of phytosociological data from oreophilous vegetation in the Apennines (Italy) has been performed. Ranking, classification and ordination methods have been used. The advantages of the joint use of the different methods is diseussed. The results confirm a compositional gradient related to degradation due to grazing, and another, related to base-richness in the soil. Compositional variation does not appear strongly disjointed.Nomenclature follows Zangheri (1976)This work was supported by a grant from the Italian CNR, Pfoject Environment Quality. We wish to thank Professor L. Orlóci for discussions and facllities, and Drs. D. Ubaldi and C. Ferrari for participation in the fieldwork.     

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.     

Leaf and canopy adaptations in a high-elevation desert on Tenerife,Canary Islands

Quantitative data on the morphology of leaves and canopy in a high elevation desert stand on Tenerife have been analyzed by multivariate methods. The results show a trend in morphological variation that is related to plant height. An interpretation of this trend in terms of the adaptive values of different character combinations suggests that this could be related to a vertical microclimatic gradient. Three main groups of species have been identified, which have evolved different adaptive strategies to different niches within a single stand. The functional values of the character combinations of each species group are discussed.Nomenclature follows Bramwell & Bramwell (1983).This research is part of a broader co-operative project Convergent evolution of plant communities in distant areas, codirected by D. Lausi (University of Trieste, Italy) and L. Orlóci (University of W-Ontario, London, Canada), and funded by the Italian C.N.R. and the Canadian N.S.E.R.C.     

On the dynamics of vegetation: Succession in model communities

Summary Successional change is thought to be at least partially driven by forees originating from within the community, namely by reaction and competition. Both processes operate through changes in the environment, but from the literature on the subject it is not clear how they differ.To clarify these issues successiens of model communities are studied. This leads us to conclude that competition represent an instantaneous interaction, whereas reaction has historical aspects since it relies on cumulative changes in the environment. The three models considered-one relying on reaction to cause vegetational change, one relying on competition and differential growth rates, and a hybrid third one-yield very similar predictions: roughly bell-shaped curves displaced along the time axis. This shows that the mere fit of a certain model to successional data may easily be spurious (recently some workers have empirically fitted models identical to one derived here from first principles). The three models do behave radically different under perturbation, however: any model relying completely or partially on historical interactions cannot account for the well known possibility of artificially arresting succession. Even if the importance of historical interactions in succession (i.e. the Markovian character of succession) cannot easily be ascertained, one can nevertheless ask whether historical interactions are at all necessary for the explanation of successional change. It is argued here that succession can be entirely understood in terms of instantaneous interactions, notably competition. The argument rests upon the well known relationship between colonizing and competitive ability, and on the fact, proven here, that stress, defined as expressing itself in severe random fluctuations in the growth parameters, is negatively correlated with competition intensity.The author gratefully acknowledges the critical support be received from Professor László Orlóci. This paper forms part of a wider research program supported by a NCR grant to Proc. Orlóci.     

A numerical phytosociological study of the summits of the majella massive (Italy)

Summary A phytosociological study of Majella's summits by the use of multivariate methods has allowed to discover the following new associations:Gnaphalio-Plantaginetum atratae on humocarbonatic soils in snowy depressions,Leontopodio-Elynetum on rendzina in wind exposed and stony places,Saxifrago-Papaveretum julici andCrepidi-Leontodontetum montani on protorendzina with gravel.Gnaphalio-Plantaginetum atratae andLeontopodio-Elynetum might be classified inElyno-Seslerietea, although the former presents character species ofSalicetea herbaceae; Saxifrago-Papaveretum julici andCrepidi-Leontodontetum montani are classified inThlaspidion stylosi (foeder. nova) ofThlaspidietea.Comparisons between some clustering methods and between ordination methods based on the mathematics of principal component analysis are discussed. The efficiency of sum of squares agglomeration when the plant communities vary in a continuum and the importance of a linearizing transformation in principal component analysis are stressed.The research was supported by a grant from the Italian CNR to Prof. D. Lausi. We wish to thank also Prof. L. Orlóci, Dr. E. van der Maarel and Prof. S. Pignatti for reading and discussing the text, and Mr. A. Zampar, S. Sedmak and T. Ubaldini for technical assistance.     

Similarity coefficients for classifying relevés

Summary Some characteristics of the more commonly used similarity coefficients have been discussed. Coefficients with undesirable properties include: the product moment correlation coefficient, some information statistics, the relative homogeneity function, the weighted similarity coefficient, the Euclidean (absolute) distance, Gleason's, Ellenberg's and Spatz's similarity indices, and the absolute value function.Of the six coefficients that were tested with two sets of phytosociological data, the Canberra measure and the absolute Euclidean distance were the least successful, with at least one data set, in providing classifications that were similar to the classifications obtained by the Braun-Blanquet sorting technique. The standard Euclidean distance and the similarity ratio had intermediate success. The Czekanowski coefficient, especially in its relativized from (= relative absolute value function), was the most successful. This latter coefficient is cover-weighted and therefore the Canberra measure, although it has some undesirable characteristics, may be valuable for investigating relevé similarities that are based on species with low cover.The transformation of Coetzee & Werger (1973) appears to be appropriate as a conversion of the cover-abundance values. The mean cover percent values corresponding to the cover-abundance values gave poor results.The relativized Czekanowski coefficient should be suitable at the lower syntaxonomical levels. At higher levels, qualitative coefficients may be sufficient for determining similarities between syntaxa. Qualitative coefficients will not always be successful at the lower levels — this was illustrated with the test data.In this study, the clustering procedure of group average sorting was used to construct the dendrogram. It gives an average similarity value within the dendrogram groups. These values can be used to give quantitative definitions to syntaxonomic rank.This research was supported by the University of Minnesota. A grant from the UM Computer Centre is acknowledged. I am grateful to Prof. E. Cushing, Dr. E. van der Maarel, and Prof. L. Orlóci for criticism which has improved the paper.     

Classifying aquatic macrophytes as indicators of eutrophication in European lakes

Aquatic macrophytes are one of the biological quality elements in the Water Framework Directive (WFD) for which status assessments must be defined. We tested two methods to classify macrophyte species and their response to eutrophication pressure: one based on percentiles of occurrence along a phosphorous gradient and another based on trophic ranking of species using Canonical Correspondence Analyses in the ranking procedure. The methods were tested at Europe-wide, regional and national scale as well as by alkalinity category, using 1,147 lakes from 12 European states. The grouping of species as sensitive, tolerant or indifferent to eutrophication was evaluated for some taxa, such as the sensitive Chara spp. and the large isoetids, by analysing the (non-linear) response curve along a phosphorous gradient. These thresholds revealed in these response curves can be used to set boundaries among different ecological status classes. In total 48 taxa out of 114 taxa were classified identically regardless of dataset or classification method. These taxa can be considered the most consistent and reliable indicators of sensitivity or tolerance to eutrophication at European scale. Although the general response of well known indicator species seems to hold, there are many species that were evaluated differently according to the database selection and classification methods. This hampers a Europe-wide comparison of classified species lists as used for the status assessment within the WFD implementation process.     

Correlation between soil characters and forest types: a study in multiple discriminant analysis

Multiple discriminant analysis is a useful multivariate technique in vegetation studies that can be employed for several purposes, even if the underlying statistical assumptions are not satisfied. An example of application of this method is discussed: multiple discriminant analysis was successfully used for evaluating the predictivity of forest types defined by numerical classification of vegetation data with respect to soil variables.Species nomenclature follows Pignatti (1982) for vascular plants and Augier (1966) for mosses.The research has been supported by the IDROSER (Bologna, Italy) and by the Italian C. N. R. (Grant no. 83.02548.04, resp. Prof. A. Pirola). We wish to thank Prof. E. Feoli, Prof. E. van der Maarel, Prof. L. Orlóci and Prof. A. Pirola for suggestions. We are also indebted to Dr N. Filippi who analyzed the soil samples.     

Grid — A space density analysis for recognition of noda in vegetation samples

Summary Recognition of noda is performed in a point cloud of n-space using grid analysis. The input data represent coordinates, preferably component scores, to reduce dimensionality. The exact position of the noda is approximated in an iterative search procedure which allows the user-defined space segments to drift into regions of high point density. The results are independent of group size and shape and they tend to compensate for uneven sampling in the different types of the survey site. The method gives flexibility in group recognition at different resolutions and provides a practical means to handling large data sets, while at the same time producing an optimal solution. The method, suitable to be used in the place of divisive clustering algorithms, has been applied to vegetation data with success. Results from two such applications are presented.The author expresses his thanks to Dr. L. Orlóci for discussions and critical review, and to the University of Western Ontario for computer time.     

A Ranking Approach to Genomic Selection

Background

Genomic selection (GS) is a recent selective breeding method which uses predictive models based on whole-genome molecular markers. Until now, existing studies formulated GS as the problem of modeling an individual’s breeding value for a particular trait of interest, i.e., as a regression problem. To assess predictive accuracy of the model, the Pearson correlation between observed and predicted trait values was used.

Contributions

In this paper, we propose to formulate GS as the problem of ranking individuals according to their breeding value. Our proposed framework allows us to employ machine learning methods for ranking which had previously not been considered in the GS literature. To assess ranking accuracy of a model, we introduce a new measure originating from the information retrieval literature called normalized discounted cumulative gain (NDCG). NDCG rewards more strongly models which assign a high rank to individuals with high breeding value. Therefore, NDCG reflects a prerequisite objective in selective breeding: accurate selection of individuals with high breeding value.

Results

We conducted a comparison of 10 existing regression methods and 3 new ranking methods on 6 datasets, consisting of 4 plant species and 25 traits. Our experimental results suggest that tree-based ensemble methods including McRank, Random Forests and Gradient Boosting Regression Trees achieve excellent ranking accuracy. RKHS regression and RankSVM also achieve good accuracy when used with an RBF kernel. Traditional regression methods such as Bayesian lasso, wBSR and BayesC were found less suitable for ranking. Pearson correlation was found to correlate poorly with NDCG. Our study suggests two important messages. First, ranking methods are a promising research direction in GS. Second, NDCG can be a useful evaluation measure for GS.     

Phytoecological importance,mutual redundancy and phytological threshold values of certain climatic factors

A combination of methods (intensity of indication, floristic and mesological redundancy analysis, beta-diversity analysis, principal components analysis and Wildi's interactive ranking procedure) were used to evaluate redundancy and relative phytoecological importance among 80 climatic variables in Galicia (N.W. Spain). The information they contained was found to be adequately summarized by just 3 factors thought to play a major role in regulating the distribution of the species considered in the study area and similar areas: Baudiere's QE index, mean minimum temperature in the coldest month and mean temperature range in the coldest month. For these three factors, phytoclimatic thresholds were determined by examining beta-diversity and were used to define phytoclimatic zone types.

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Resumen Se valora la redundancia e importancia fitoecológica relative de 80 variables climáticas en Galicia (N.O. de España) empleando una combinacion de diferentes metodos (intensidad indicadora, análisis de la redundancia florística y mesológica, análisis de beta-diversidad, análisis de componentes principales y el método de ordenación interactiva de Wildi). La información contenida en esta variables es adecuadamente resumida por 3 factores que juegan un papel predominante en regular la distribución de las especies consideradas en el area de estudio y areas similares: el índice QE de Baudiere, la temperatura media de las mínimas del mes más frío y la oscilación térmica del mes más frío. Para estos factores el análisis de la beta-diversidad permitió determinar los umbrales fitoclimáticos utilizados en la definición y cartografía de las zonas fitoclimáticas.

     

Graphical comparison of resemblance measures in phytosociology

A simple graphical method, COREM, is described for the comparison of quantitative resemblance measures. The basis of the method is the ordered comparison case series (OCCAS) composed of relevé pairs ranked in decreasing order of similarity. For a given OCCAS, values of given resemblance functions are calculated and plotted in COREM.Delta resemblance (DR) is defined as the rate of change between two neighbouring relevé pairs in the OCCAS. High mean delta resemblance (% MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqaqpepeea0xe9qqVa0l% b9peea0lb9sq-JfrVkFHe9peea0dXdarVe0Fb9pgea0xa9pue9Fve9% Ffc8meGabaqaciGacaGaaeqabaWaaeaaeaaakeaadaqdaaqaaGqaai% aa-reacaWFsbaaaaaa!392E!\[\overline DR \]) of a resemblance measure indicates a high power of resolution and small standard deviation (SDDR) is indicative of linearity. A measure of efficiency combines % MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqaqpepeea0xe9qqVa0l% b9peea0lb9sq-JfrVkFHe9peea0dXdarVe0Fb9pgea0xa9pue9Fve9% Ffc8meGabaqaciGacaGaaeqabaWaaeaaeaaakeaadaqdaaqaaGqaai% aa-reacaWFsbaaaaaa!392E!\[\overline DR \] and SDDR in the coefficient of variation for delta resemblance (CVDR). An efficient measure shows balanced sensitivity to the common and differential species. With the method COREM locally optimal resemblance measures may be selected for any given set of relevés which produce the sharpest separation of clusters. A reasonable compromise is to use types of measures, such as the similarity ratio (SIM6), Czekanowski coefficient (SIM8), or floristic similarity (SIM9), which have the best chance of being successful in most relevé sets. A study of transformation functions on Braun-Blanquet values with the help of COREM demonstrates that the combined transformation is the most advantageous for clustering. It is shown that standardization by relevés, or conversion to unit sum has undesirable effects.During the preparation of this paper the author was a recipient of a Postgraduate Scholarship, Deutscher Akademischer Austauschdients, Dortmund, KFA Abteilung Algenforschung, Germany. The author would like to thank L. Orlóci, P. Juhász-Nagy and E. van der Maarel for valuable suggestions, and comments.     

Des considérations écologiques peuvent-elles apporter une contribution a la connaissance du cycle biologique des colonies deCremastogaster (Hymenoptera-Formicoidea)?

Resumen Ciertos nùmeros de luchos experimentales y de observación de cuatro especies deCremastogaster: Cr. auberti, Cr. scutellaris (de Francia);Cr. vandeli, Cr. skounensis (de Cambodia) han conducido a formular una hipotesis acerca del ciclo biologico de ciertos especies deCremastogaster.Hay alternancia entre dos generaciones, una agama reproduciéndose por partenogenesis, otra sexuada. La generación sexuada comprende machos y hembras aladas destinadas al origen para la diseminación del especie aprovechando las condiciones ecológicas favorables (vuelo de enjambre). La descendencia normal de las hembras est a constituida por obreras (sin embargo puede haber en las hembras partenogenesis arrhenotoque accidental del tipo himenoptere). La generación agama comprende solo hembras apteras (obreras) y està destinada para la conservación del especie durante las estationes con condiciones ecológicas defavorables. Esas obreras son poco prolificas y ciertamente solo por un breve periódo de su vida. La generación asexuada vuelve a dar una generación sexuada por partenogenesis deuterotoque (La deuterotoquia està bajo la influencia de factores troficos y, por consiguiente, ecológicos).

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Summary Some number of expérimental samples and observations on for species ofCremastogaster: Cr. auberti; Cr. scutellaris (of France);Cr. vandeli, Cr. skounensis (of Cambodia) brings to formule hypothesis on biological cycle of some species ofCremastogaster.There is alternance between two generations, the one without sexual types, which reproduces by parthenogenesis, the other with sexual types. The sexual generation comports winged males and winged females for dispersion of species (in beginning) which profit of ecological favourable conditions (wing of swarming). The normal descendance of females is constitued by workers (however by males it can existe accidental arrhenotocal parthenogenesis of Hymenopteral type). The without sexuals generation comports only wingless females (workers) and it is destined to conserve the species during seasons under unfavourable ecological conditions. These workers are not to much prolific and certainly during a short time of their life. The asexual generation gives again sexual generation by deuterotocal parthenogenesis (Deuterotoquia is under the influence of trophic and, from this fact, ecological factors).

     

Quantitative phytogeography of the Yukon Territory (NW Canada) on a chorological-phytosociological basis

This study is based on the analysis of the chorological spectra from 19 vegetation types obtained from a numerical classification of ca. 400 phytosociological relevés taken during a vegetation survey in the Yukon Territory (NW Canada).All vegetation types are well characterized in terms of their chorological features. This allowed an ecological-historical interpretation of the vegetation in the study area. The distribution of the various chorological categories within the vegetation types is strongly correlated with the main environmental influences, whose action led to the present floristical and vegetational characteristics of the area, such as glaciation, fire, permafrost and water availability.The results show how the phytosociological approach constitutes an effective methodological tool for clarifying the phytogeographical aspects in the historical-ecological interpretation of a large area.Nomenclature follows Hultén (1968), otherwise author names are specified.The field work was completed in the summer of 1978. We are grateful to Dr W. Stanek, Canadian Forestry Service, for coordination of the survey and for soil data, and to Prof. L. Orlóci for organization. Partial financial support was received from the Italian C.N.R.     

Releve ranking based on a sum of squares criterion

Summary When a very large number of phytosociological types have to be compared, a reduction of the number of relevés is desirable. In this paper a method of relevé selection from given phytosociological tables is suggested. The method is based on a sum of squares criterion. The advantage, in comparison with other selection procedures, is that this method provides a means on the basis of which the efficiency of a relevé selection can be objectively measured.Contribution from the Working Group for Data-Processing in Phytosociology, International Society for Vegetation Science.The work was completed at the Department of Plant Sciences of the University of Western Ontario, London, Canada. We wish to thank Prof. L. Orlóci for the hospitality and the helpful discussions. The work was supported by Italian C.N.R., within the project Promozione qualità dell'ambiente subproject Metodologie matematiche e basi di dati.