Narrow Results

The crucial role played by the analysis of microbial diversity in biotechnology-based innovations has increased the interest in the microbial taxonomy research area. Phylogenetic sequence analyses have contributed significantly to the advances in this field, also in the view of the large amount of sequence data collected in recent years. Phylogenetic analyses could be realized on the basis of protein-encoding nucleotide sequences or encoded amino acid molecules: these two mechanisms present different peculiarities, still starting from two alternative representations of the same information. This complementarity could be exploited to achieve a multimodal phylogenetic scheme that is able to integrate gene and protein information in order to realize a single final tree. This aspect has been poorly addressed in the literature. In this paper, we propose to integrate the two phylogenetic analyses using basic schemes derived from the multimodality fusion theory (or multiclassifier systems theory), a well-founded and rigorous branch for which its powerfulness has already been demonstrated in other pattern recognition contexts. The proposed approach could be applied to distance matrix–based phylogenetic techniques (like neighbor joining), resulting in a smart and fast method. The proposed methodology has been tested in a real case involving sequences of some species of lactic acid bacteria. With this dataset, both nucleotide sequence– and amino acid sequence–based phylogenetic analyses present some drawbacks, which are overcome with the multimodal analysis.

Whole organism anatomical data are usually examined with specific hypotheses in mind: specifically that they are testing ideas about functional adaptations, convergences and parallels, or about primitivenesses, derivednesses and phylogeny. Presumably, of course, such data actually contain information about all of these factors. In addition, because they describe the end result of genetic mechanisms and developmental processes, they should be reflecting these in some degree. The separations of many such factors is very difficult as long as investigation is confined to individual anatomical observations (often called characters) because they will usually contain mixtures of information of various kinds. In data that are rendered quantitatively, however, it seems possible that statistical treatment might allow a degree of disentangling of these various factors. For studies of humans, the situation is especially complex because, though some investigations emphasises the adaptive uniqueness of humans from all other primates, related generally to their unique adaptations, other studies mirror the genetic closeness of humans to other primates, especially, of course, the African great apes.

This investigation looks at several quantitative studies of whole organism structure that, on the face of it, seem to present easily recognisable functional information. It tries to discover, both through the addition of individual studies into combined investigations, and by examining clusters of variables as well as clusters of animals, the degree to which the information content is really more complex. The various studies include morphometrics of the postcranium, cranium and teeth, but they also extend into the anatomy of the niche (hence nichemetrics) and into the form and proportions of the brain (hence ‘neurometrics’). The end result seems to be that a degree of disentanglement is indeed possible and that developmental phenomena obtained from studies of individual experimental animals are reflected in whole organism data from the adults of a wide diversity of related species. This result also speaks, therefore, about why humans hold paradoxical positions in different studies.

The aim of this study is focused in the evaluation of the genetic diversity of C. violaceum isolated from Brazilian ecosystems. Strains from Malaysia, Amazonas, Pernambuco, Ceará were analysed by the 16S rRNA gene (amplified 16S ribosomal DNA restriction analysis) to define their phylogenetic positions. All strains were grown overnight in LB medium at 30°C at 150 rpm, and cooled on ice, and the DNA was amplified in a thermocycler. The primers used were fD1 (AGAGTTTGATCCTGGCTC AG) and rD1 (AAGGAGGTGATCCAGCC) complementary to the ends of the 16S rDNA. The data obtained herein demonstrated that this method allowed grouping the C. violaceum isolates according to different Brazil States. However, the distances genetics between among all the isolated ones studied in this work demonstrated low variability but that the use of 16S rDNA gene tree revealed the good correlation between phylogenetic clustering and geographic origin.