chloroplast and other genes (was Lucy in Newsweek)

[Richard Pyle]

> I was with you until this point, but now I have to object strenuously.
> There are no "discrete phylogenies". Phylogeny is our interpretation of a
> historical pattern,

Yes, but a historical pattern of what?  Molecules? Genes? Genomes?
Organisms? Populations? Taxa?  I concede that my philosophical ramblings on
this are almost entirely moot, because we all sort of "know" what we mean by
evolutionary history.  But I think we may eventually find that the devil is
in the details.

> and in the case of sexually reproducing eukaryotes,
> *that pattern is the result of species*.

No.  That pattern is the result of individual organisms recombining genetic
information through a perpetual cycle of matter assemblage and entropy.

> The phylogeny that morphological cladists look at is the species tree, and
that tree is the
> *consequence* of speciation, at least in the sense that speciation means
lineage-splitting
> (which to me is its most useful definition).

If you trace the pedigree of two individuals from two separate species back
in history to the point where they share a single ancestor individual in
common (i.e., a "Lucy", to bring this back to relevance with the subject
line), you'll find in virtually every case that that specific individual was
surrounded by a broad population of individuals; some of whose genetic
material may have recombined with descendents of the "Lucy", and some of
whose did not.  I defy you to define a discrete point at which two species
lineages actually diverged.

> Despite the fact that many of us talk about "the true phylogeny", what we
> are really after is the ability to make consistent and reproducible
> inferences about specific aspects of history.

On this point, we are in near complete agreement!  I'm not sure, exactly,
how you define "reproducible" in this sense (except maybe that if you
sequence the DNA of a particular organism twice on the same section of the
genome, you'll get the same sequence both times; or perhaps if you define a
morphological character, you'll see find it in more than one individual
organism).  I would be more inclined to describe it as "consilience".  That
is, when there is a strong consilience of evidence (among and within
different lines of evidence from morphology, genetics, fossil record, etc.)
that points to the same pattern of relationships, then our confidence in the
inferred phylogeny is relatively high.  When the consilience is less perfect
(as seems to be the case with primates), we should be less confident in our
alternative convictions.  When consilience is low, then we should have
confidence only in the fact that we really have no idea what the "true"
phylogeny is.

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