Joined: May 2002
I noticed Charlesbois's article also, comments are here:
Re-evolution of complex characters
IMO this quote is the key one for putting some balance into discussions where Woese, Doolittle, etc. are cited:
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. The input data for genome trees can be the proportions of genes or proteins that genomes hold in common, or (as we prefer) the mean pairwise similarities between shared proteins. Despite some early indications to the contrary, whole-genome trees have now largely converged on the rRNA-sequence tree.
For us — as, presumably, for the verticalists — 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. Lateral transfer is not both quantitatively important and directional. One of the few widely accepted instances of lateral gene transfer — the origin of chloroplasts from relatives of cyanobacteria — is clearly visible in our whole-genome trees, and even more so in 'sub-genome trees' based on functional subsets of genomes.
Edited by niiicholas on Jan. 18 2003,23:54