>I would suspect that given greater importance of horizontal gene transfer
>(HGT) in bacteria that the signal would be more blurred in bacteria rather
>than in higher organisms. So your skepticism of the application of
>phylogenies based on sequence data is unfounded.
You're probably right, but I wouldn't be so sure. Remember, that
prior to sequencing these genomes, everyone expected to
decipher the last common ancestral state of bacteria. It was indeed a
surprise to find we couldn't and this has been a huge impetus behind
citing HGT as of such importance (prior to genomics, most were
skeptical). The same pattern may repeat itself. Yes, it is true
metazoans don't have two of the HGT mechanisms (conjugation
and transformation), but viral vectors remain a plausible possibility,
especially in light of the ubquitious "junk" DNA (amplified leftovers
of viral insertations??) that seems to characterize these genomes
(and the manner in which epigenetic mechanisms seem to be
"defense mechanisms" against such invasion). Of course, it will be
some time before we have enough metazoan genomes to make such
conclusions.
>Of course, the fact that HGT is so important and evident in bacteria
>provides for non-Darwinian evolutionary mechanisms that produce complex
>systems.
In some ways, HGT is at significant tension with classical Darwinian
views of evolution. But I don't know of any evidence that HGT has
ever *produced* a complex system. It spreads them about (highlighting
just how modular life is), but produces them?
Mike