A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data

Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits—a more or less subjective element of the framework—remains to be investigated

Spatial Processes In The Analysis Of Vegetation

Vegetation Science often relies on methods whose principal strategy involves the change of some parameters of sampling. There is, in fact, a time-static spatial dynamism in the analysis of vegetation, and most changes can be ordered into a sequence, whereby spatial processes are defined. The objective of the present thesis is to create a theoretical framework for the discussion and review of time-static spatial processes, to give a methodological basis for their analysis, and to illustrate some possibilities through real and simulated examples.;Two basic types of processes are distinguished: (1) the primary processes defined by the investigator, and (2) the dependent processes automatically generated once a primary process is defined. Within these, further distinction is made based on the type of space with which the process is associated, and the number of controlling parameters.;The role of primary and dependent processes is investigated in real, data, resemblance, classification, and ordination spaces, and in the space of derived variables. Past contributions to the topic and the task of analyzing spatial processes are reviewed. It is stressed, and demonstrated, that the study of spatial processes is, or should be, a vital part in: (1) the optimization of sampling design for statistical estimation or typification; (2) the optimization of data type to reduce sampling effort and cost; (3) the reduction of large data sets to permit computerized analysis; (4) the detection of pattern in a single or a multi-species plant population; (5) the analysis of interspecific relationships; (6) the control of the stability of ordinations and classifications; (7) the determination of the relative impact of different processes upon the results; (8) the performance of pilot studies prior to the analysis of temporal changes in vegetation; (9) the recognition of trends in the results; and in (10) the discovery of the principal characteristics of the vegetation

The Coral of Life

The Tree of Life (ToL) has been of central importance in the biological sciences, usually understood as a model or a metaphor, and portrayed in various graphical forms to summarize the history of life as a single diagram. If it is seen as a mathematical construct—a rooted graph theoretical tree or, as more recently viewed, a directed network [Network of Life (NoL)]—then its proper visualization is not feasible, for both epistemological and technical reasons. As an overview included in this study demonstrates, published ToLs and NoLs are extremely diverse in appearance and content, and they suffer from inevitable bias towards particular groups, or are restricted to a single major taxon. Metaphorical trees are even less useful for the purpose, because ramification is the only property of botanical trees that may be interpreted in an evolutionary or phylogenetic context. This paper argues that corals, as suggested by Darwin in his early notebooks, are superior to trees as metaphors, and may also be used as mathematical models. A coral diagram is useful for portraying past and present life because it is suitable: (1) to illustrate bifurcations and anastomoses, (2) to depict species richness of taxa proportionately, (3) to show chronology, extinct taxa and major evolutionary innovations, (4) to express taxonomic continuity, (5) to expand particulars due to its self-similarity, and (6) to accommodate a genealogy-based, rank-free classification. This paper is supplemented with a figure, The Coral of Life (CoL), which is, to the author’s knowledge, the first attempt to combine all of the above features in a single diagram for the entirety of life, thus serving as a prototype for further analysis and improvement. The discussion is partly historical: references to classical and modern writings help the reader to understand how biological thinking and methods of visualization have evolved to reach this achievement

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

Southern Thailand bryophytes II

Abstract The collection of epiphyllous bryophytes in the lowland rainforests of Phang-Nga province and in the neighbouring Phuket and Surat Thani provinces resulted in 54 liverwort and one moss species, of which 14 are new records for the bryoflora of Thailand. Epiphyllous bryophyte assemblages from nine localities are evaluated for species richness and beta diversity, as well as for their phytogeographical status

Többváltozós ökológiai mintázatok értékelése: új módszerek = New methods for the analysis of multivariate data in ecology

Új algoritmust dolgoztunk ki prezencia-abszencia ökológiai adatmátrixok randomizálására. Magyarországi sziklagyepek északi és déli lejtőinek magtömeg-spektrumát elemeztük. Új eljárást, az "adjacency analysis" -t dolgoztunk ki, amely permanens kvadrátok időbeli változásainak elemzésére alkalmas, igy használható eszköz a szukcessziós folyamatok kutatásában. Növények térbeli mintázatának elemzésére alkalmas eljárást fejlesztettünk ki, amely a Boole algebrán alapszik. A tabelláris átrendezések optimalizációjára adunk eljárást, melyben a Markov Chain Monte Carlo algoritmust alkalmazzuk. Az ordinális adatok többváltozós feldolgozásának lehetőségeiről és új eljárásokról irtunk review-t. A diverzitásfüggvények egy egyszerű kiterjesztését javasoltuk a folyotonos esetre. Tanulmányt készítettünk a térbeli autokorreláció, a kvadrátméret és az osztályozások kapcsolatáról. Táplálékhálózatok és hálózati indexek többváltozós értékelését hajtottuk végre több tanulmányban. A funkcionális diverzitás dendrogramokból való számolásának egységesítését javasoltuk a Gower index és az UPGA osztályozó módszer felhasználásával. Megvizsgáltuk, hogy a Calamagrostis epigejos nevű klonális fűfaj dominanciája mennyire befolyásolja más fajok turnover-ét egy löszgyepi társulásban. A funkcionális diverzitás mérésében általánosan alkalmazott "functional attribute diversity" nevű mérőszám egy módosítását is javasoltuk. Több könyvfejezet és könyv is elkészült a pályázat futamideje alatt. | A new algorithm has been developed for randomizing presence-absence data matrices. The seed mass spectra of rock grasslands on southern and northern slopes were compared. A new method, adjacency analysis is developed for the evaluation of temporal vegetation changes through permanent quadrats, which is useful for the study of successional processes. A new pattern analysis method is developed based on Boolean algebra. The Markov chain Monte Carlo method is suggested to rearrange ecological data matrices. A review has been written and new methods suggested for the analysis of multivariate ordinal data. Diversity functions are expanded to handle the continuous situation as well, so that no classification is necessary. We examined the relationship between quadrat size, spatial autocorrelation and classification of vegetation. Food webs and web indices were also evaluated using multivariate techniques. The calculation of functional diversity from dendrograms is proposed based on the Gower index and the UPGMA method. The effect of a clonal plant on species turnover was examined in a loess grassland community. The functional attribute diversity measure is modified to cope with the twinning problem. Several books and book chapters complete the list of publications