Hotel Estoril Eden, Monte Estoril,
Portugal
5-8 October 2005

 

 
 

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P
hylogenies, Genome Organization and Taxonomy in Prokaryotes: Dream or Reality?

Rogério Tenreiro
University of Lisbon, Department of Plant Biology, Portugal

Molecular phylogenetic analysis is an important issue in microbiology, enabling the inference of evolutionary relationships among microorganisms and setting up a natural-assumed framework for definition of taxonomical groups at hierarchic classification levels. Beyond this systematics-oriented approach, molecular phylogenies can be used to predict equivalent gene functions, to unravel clonal relationships among microbial isolates in an epidemiological context and to understand genome evolution.

Reconstruction of phylogenies can be performed with several kinds of molecular data (both at DNA or protein level) and a panoply of inferential approaches that includes character-based, distance-based and statistical methods. Unfortunately, inferred phylogenetic trees may depend both on the selected molecular marker and the inference method.

Prokaryotic genomes evolve by several genetic mechanisms leading from minor changes to extensive rearrangements that are mainly vertically inherited. However, genes may be under different selective pressures and so may display different evolution rates. Furthermore, horizontal gene transfer among prokaryotes seems to play a more important role in prokaryote evolution than initially expected, as deduced from comparison of available full-genome sequences.

Taking in account all this information, a polyphasic strategy based on several molecular markers and distinct inference methods seems to be an appropriate choice to obtain a more reliable and congruent phylogeny in order to assess taxonomical relationships among prokaryotic groups. To illustrate these issues, two examples will be presented: one regarding the comparison between genome organization and phylogenies at intra-specific level in lactic acid bacteria and the other concerning the congruence among phylogenies based on distinct genes in rickettsial species.

The development of inference methods for simultaneous multi-targeted phylogenies and robust congruence evaluation methods will also be presented as a final challenge.