An ecological example of the application of projection pursuit to compositional data

A modern statistical technique for the exploratory analysis of multivariate data, called projection pursuit, is described. The method consists of the extraction and display of informative one- or two-dimensional projections of the multivariate dataset. Projection pursuit has much scope for application to ecological datasets. The example in this paper concerns element concentrations in soil samples from a coastal embayment on the east coast of Australia. The application attempts to search for patterns in the soils which could be related to vegetation patterns. The compositional nature of the dataset adds a novel element to the methodology.     

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities

The profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from known X-ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (alpha-helix, beta-strand or "other") is assigned to each position of the aligned sequences. As in the standard profile method, a position-dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in alpha-helices, beta-strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure-based profile method, we created a profile for eight-stranded, antiparallel beta barrels of the insecticyanin folding class. It is based on the sequences of retinol-binding protein, insecticyanin and beta-lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel beta barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.     

Racemization of the aqua-{N-salicylidene-(S)-alaninato}copper(II) by reaction with potassium cyanate

Copper(II) N-salicylidene-(S)-alaninate trihydrate reacting as the S-enantiomeric parent compound with KOCN in hot diluted methanol yielded by slow crystallisation from the cooled reaction mixture (in the course of 1 day) the racemic product K[Cu{sal-(RS)-ala}(NCO)]. The parameters of the axial type EPR spectrum in X-band region and the LF band position in the electronic spectrum are typical of an axially distorted square pyramidal coordination of the Cu(II) atom in this complex. The spectral properties of the complex cuprate prepared and its basal crystallographic data are consistent with those of the earlier studied¹⁵ K₂[Cu₂{sal-(RS)-ala}₂(μ-NCO)₂] synthetized by using [Cu{sal-(RS)-ala}(H₂O)].H₂O as the racemic parent complex in the reaction mixture with KOCN.     

Dynamics of distribution in animal communities: Theory and analysis

Theoretical and analytical problems of the dynamics of distribution and abundance in animal communities were examined. In many communities, species with low abundance and of limited spatial occurrence (i.e., rare species) typically form a conspicuous peak when a frequency distribution of the number of species is constructed with respect to the proportion of sites occupied within an area of distribution. Models of distribution dynamics, including a new model proposed here, were compared with a range of animal community data using a new procedure to assess single- and bi-modal patterns in frequency distributions of spatial occurrence. Data reveal that single-modality with an excess of rare species occurs more frequently than bimodality. Even when bimodality is detected, the mode representing wide-spread species is in the majority of cases smaller than that for rare species. Thus, a new model in which the rate of local extinctions is assumed to be negatively related to patch occupancy (or population abundance) is in better agreement with observed data than earlier models. Some problems of analysis, in particular model assumptions and testing, are discussed.     

Book reviews

Editing of community data matrices is complementary to analyzing data by multivariate techniques of classification and ordination in the overall task of data analysis. A computer program, DATAEDIT, is described that can perform numerous editing functions, including data transformation, deletion of certain species or samples, deletion of rare species, deletion of outliers, separation of disjunet sample groups, reordering of the species or samples of a data matrix, and the formation of composite samples or of sample subsets. DATAEDIT can use the information in a nonhierarchical or hierarchical classification, and includes its own internal routine for reciprocal averaging ordination.We appreciate valuable suggestions from the late Robert H. Whittaker, and from Philip Dixon, David Hieks, Laura Huenneke, Linda Olsvig-whittaker, and Mark Wilson. Mark O. Hill kindly supplied a fast subroutine for reciprocal averaging.