chloroplast and other genes (was Lucy in Newsweek)

[Richard Pyle]

> Of course, many molecular branch arrangements agree with morphological
> arrangements, but why can't there be problematic taxa that simply can't be
> phylogenetically resolved?

I see this as a very real possibility; i.e., that the confidence "asymptote"
may prove to be lower than we would all like it to be.  I suspect confidence
levels will be lowest for those sorts of organisms with relatively small and
"tight" genomes (e.g., prokaryotes).  In other words, some amount of
phylogenetic information is undoubtedly lost; probably forever (except,
perhaps, for the inferences that we might be able to make from fossil
morphology and/or other lines of non-genomic evidence).  In that scenario, I
fear we are pretty-much "S.O.L."

But my contention has been, and is, that whatever the extent to which the
information exists at all, it exists in the genome. If it's not somewhere in
the genome (irrespective of our current ability to extract that
information), then it is certainly not going to exist in the morphology (or
behavior), because the phylogenetially informative aspects of morphology and
behavior are, almost by definition, those that are coded for by the genome.
In other words, if we're going to attempt to reconstruct evolutionary
history, we are (for the most part) confined to the remnants of information
that have been passed from generation to generation over the history of life
on Earth -- and most of that information (nearly all of it) is contained
within the gametes of sexually reproducing organisms, and the
information-bearing cellular components of asexual reproducers.

My contention has further been, and is, that passionate arguments about
"true" phylogenies are sort of like a bunch of 3rd-graders trying to
describe quantum physics.  We are just now beginning to realize how little
we actually understand about what information is, and is not, locked up
somewhere in the genome.  The more we realize this, the less confident we
should be in any of our inferences about the historical pathways by which
the genomic (and presumed morphological manifestations thereof) information
trails have followed.

Time for me to go back to my safe, cozy, alpha taxonomy....

Aloha,
Rich

=======================================================
Richard L. Pyle, PhD
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://www.bishopmuseum.org/bishop/HBS/pylerichard.html