Joined: Oct. 2002
A good short commentary by Charlebois et al on the issue of microbial phylogenetic trees is found in this week's Nature.
|We and others have been exploring 'whole-genome trees' as a means of overcoming the noise and bias of single-protein analyses, to extract the bulk phylogenetic signals that are inherent in genomes. ...... Despite some early indications to the contrary, whole-genome trees have now largely converged on the rRNA-sequence tree.|
For us .... this convergence means that lateral gene transfer has not undermined descent with modification as the default explanation for microbial biodiversity, nor (as recently suggested by Ford Doolittle) has it thrown microbial classification into disarray. ......
The most enthusiastic lateralists reply, however, that convergence between whole-genome and rRNA trees merely demonstrates that rRNA genes — unlike most individual protein-coding genes, but like the genome as a whole — are but pastiches that are produced by lateral gene transfer.
Fascinating as these conflicts are, the important point is not whether a given tree is right or wrong. Rather, we should use these trees as frameworks upon which to construct and test hypotheses about the rate and mode of microbial evolution, and to improve our analytical methods. Without conflicts, we might all be far more complacent about evolutionary theory. In microbial phylogenomics, the scientific process is alive and well!