Showing papers on "Dendrogram published in 1996"

Grid-clustering: an efficient hierarchical clustering method for very large data sets

Abstract: Clustering is a common technique for the analysis of large images. In this paper a new approach to hierarchical clustering of very large data sets is presented. The GRIDCLUS algorithm uses a multidimensional grid data structure to organize the value space surrounding the pattern values, rather than to organize the patterns themselves. The patterns are grouped into blocks and clustered with respect to the blocks by a topological neighbor search algorithm. The runtime behavior of the algorithm outperforms all conventional hierarchical methods. A comparison of execution times to those of other commonly used clustering algorithms, and a heuristic runtime analysis are presented.

Can the spread of agriculture in Europe be followed by tracing the spread of the weed Silene latifolia. A RAPD study.

Abstract: On the basis of gene frequency data of three flavone glycosylating genes, populations of the agricultural weed Silene latifolia (Caryophyllaceae) in Europe can be divided into two chemical races: an eastern and a western race. Morphological data also show a clear east-west division. When the two datasets are combined at least nine different geographical races can be distinguished using cluster analysis. Because these observations are hard to explain by selection, it has been proposed that these different races probably originated as a consequence of migration during the spread of agriculture over Europe in the past. To discriminate between selection and genetic drift many more selectively neutral easy-to-score characters are needed. In order to test whether random amplified polymorphic DNAs (RAPDs) might be suitable for this purpose, we performed a small-scale RAPD analysis on 16 geographical different populations. Using Jaccard's coefficient of similarity, we calculated genetic distances by pair-wise comparisons of both unique and shared amplification products, and a dendrogram was subsequently constructed using an unweighted pair-group method with arithmetical averages (UPGMA). On the basis of the dendrogram two clusters were discerned that clearly coincide with the aforementioned east-west division in populations. As there has been little or no artificial selection on this weed, its migration routes may be a good reflection of the different geographical routes agriculture has taken. We propose that a phylogenetic analysis of RAPD data of many more populations may provide additional information on the spread of agriculture over Europe.

Classification of Species in the Genus Penicillium by Curie Point Pyrolysis/Mass Spectrometry Followed by Multivariate Analysis and Artificial Neural Networks

Abstract: Curie point pyrolysis/mass spectrometry of Penicillium species was performed with 530 degrees C Curie point foils. The mass spectra were submitted to principal component analysis, canonical variates analysis and hierarchical cluster analysis, producing a final dendrogram by the use of average linkage clustering. By this approach a successful classification of the species Penicillium italicum, P. expansum and P. digitatum originating from fruits was obtained. Isolates of the same species grouped together in the dendrogram, while the different species were distinguished. Also when grown on two different agar media, replicates of the same species grouped together. Likewise, a satisfactory classification was achieved by multivariate analysis of the data for various isolates of the cheese-associated fungi Aspergillus versicolor, P. discolor, P. roqueforti, P. solitum, P. verrucosum, P. commune and P. palitans. However, some difficulties appeared in distinguishing the closely related species P. commune and P. palitans. Such difficulties became greater on including more isolates and limiting the analysis to five of the species. The use of back-propagation artificial neural networks, in contrast, resulted in a correct classification in all cases. Thus, it is concluded that Curie point pyrolysis/mass spectrometry is useful in chemotaxonomic studies of the closely related species in the genus Penicillium.

Cluster analysis of 36 Globodera pallida field populations using two sets of molecular markers.

Abstract: Thirty-six populations of the potato cyst nematodeGlobodera pallida, all collected in the Netherlands, were analysed twice: by two-dimensional gel electrophoresis of proteins (2-DGE) and by random amplified polymorphic DNA fingerprinting (RAPD). Two-DGE revealed frequencies of 21 alleles at eight putative loci in each population. The same populations were subjected to RAPD analysis. This qualitative technique revealed 38 polymorphic DNA fragments. Both datasets were independently processed to determine the intraspecific variation. UPGMA analysis resulted in a 2-DGE- and a RAPD-based dendrogram with cophenetic correlation coefficients of 0.755 and 0.838 respectively. The correlation between the genetic similarity values for the populations was 0.572. Comparison between the 2-DGE- and the RAPD-based dendrogram revealed that only thirteen of the 36 populations analysed were clustered identically. It is concluded that the gene pool similarity concept is only in some instances applicable to Dutch populations ofG. pallida. For populations that could not be differentiated unequivocally on the basis of molecular markers, markers closely linked to avirulence genes should be identified. Approaches that will lead to the identification of such markers are discussed.

The genetic polymorphism of the grape studied by RAPD analysis

Abstract: Genetic polymorphism in plant of 3 genera of Vitaceae family, 11 species of Vitis genera, 10 cultivars of Vitis vinifera and 4 cultivars that obtained from distant hybridization was studied. According to date of RAPD analysis genetic distances were determined and phylogenetic dendrogram was constructed. The possibility of using PCR for evaluation of breeding material by the levels of genetic relations was shown.