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

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

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

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

Functional diversity: a review of methodology and current knowledge in freshwater macroinvertebrate research

Although several studies have examined the functional diversity of freshwater macroinvertebrates, the variety of methodologies combined with the absence of a synthetic review make our understanding of this field incomplete. Therefore, we reviewed the current methodology for assessing functional diversity in freshwater macroinvertebrate research. Our review showed that most papers quantified functional diversity using biological traits, among which feeding habits were the most common traits probably due to the assumed links between feeding and ecosystem functions. A large number of diversity measures have been applied for quantifying functional diversity of freshwater macroinvertebrate assemblages, among which Rao’s quadratic entropy looks like the most frequent. In most papers, functional diversity was positively related to taxon richness, and functional redundancy was a key concept in explaining this correlation. Most studies detected strong influence of the environmental factors as well as human impact on functional diversity. Finally, our review revealed that functional diversity research is biased towards European running waters and is hindered by yet insufficient information on the autecology of macroinvertebrates. © 2016 The Author(s