chloroplast and other genes (was Lucy in Newsweek)

[Richard Pyle]

> >Yes, but a historical pattern of what?  Molecules? Genes? Genomes?
> >Organisms? Populations? Taxa?
>
> All of the above. Certainly all those things are of interest.

How confident are you that all these patterns are going to be exactly the
same?  How often do publications dealing with phylogenetic patterns identify
which one their evidence pertains to?

> > > 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.
>
> Wrong, but thanks for playing.

Wrong?  Which part?  Individual organisms do recombine genetic information
when they sexually reproduce by combining gametes -- do they not?  Embryonic
development and subsequent organismal growth does indeed represent the
assemblage of matter -- doesn't it?  Over the course of an organism's life,
entropy is always at play (especially after an organism dies) -- correct?
So I can only assume the part that is "wrong" is that these processes are
what form the basis of the "pattern".  But to maintain that the evolutionary
pattern is *not* based on reproducing organisms seems a bit absurd to me --
so I guess there must be some miscommunication at play here.

> Genetic recombination in sexual organisms
> results in a network, not a tree.

Weird -- that was my point exactly.  I guess that means we're both wrong????

:-)

> >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.
>
> When they produce a phylogenetic signal. That seems obvious to
> me. Gradual
> continua are not at issue here; what we are looking at is the
> pattern they
> produce over time.

I have no quarrel with this, but we just don't seem to all be in agreement
of what we mean by "pattern".  A cladogram represents a pattern.  In its
simplest (and most useful) form, a cladogram showing the pattern of ((A,B)C)
implies that the pedigrees of any given individual in the scope of organisms
represented by the label "A", and of any given individual in the scope of
organisms represented by the label "B", share a more recent individual
organism in common than the pedigree of any given individual in the scope of
organisms represented by the label "C".  But that's a terribly long
sentence, so we condense it into the shorthand statement that "Species 'A'
and species 'B' share a more recent common ancestor than species 'C'."  For
the most part, this shorthand language is perfectly fine, because it
represents virtually the same thing as the more excruciating (but more
precise) version.  The danger, though, is that by only using the shorthand
version, and forgetting what it really is that we are saying, we risk
falling into the trap of thinking of the concepts of 'A', 'B', and 'C' as
"real" entities, with discrete boundaries.

Let me re-state the long version, as well as two more variants of it.

1. The pedigrees of any given individual in the scope of organisms
represented by the label "A", and of any given individual in the scope of
organisms represented by the label "B", share a more recent individual
organism in common than the pedigree of any given individual in the scope of
organisms represented by the label "C".

2. The genetic sequences of the Cytochrome-B gene of any given individual in
the scope of organisms represented by the label "A", and of any given
individual in the scope of organisms represented by the label "B", have
fewer differences from each other than either does with the sequence of the
Cytochrome-B gene of any given individual in the scope of organisms
represented by the label "C".

3. The sets of apomorphic characters of any given individual in the scope of
organisms represented by the label "A", and of any given individual in the
scope of organisms represented by the label "B", are more congruent with
each other than either is with the set of apomorphic characters of any given
individual in the scope of organisms represented by the label "C".

My question is, do all three of these statements equally collapse into the
simplified statement, "Species 'A' and species 'B' are more closely related
to each other than either is to species 'C'"? I'm not so sure -- at least
not in all cases.  But more fundamentally, I'm not sure that we always
understand what we mean by the concept of "more closely related".

For example, most of us think of number 1 above as what we're all really
trying to elucidate when we talk about phylogenies (hence my emphasis on
individual organisms and pedigrees). But suppose we re-stated number 2 above
by switching the letters "B" and "C".  Taken together, statements 2 & 3
would then appear to be in conflict with each other. The Morphologists and
the Molecularists would argue about which of the following condensed
statements is "right", and which is "wrong":

"Species 'A' and species 'B' are more closely related to each other than
either is to species 'C'"

-- OR --

"Species 'A' and species 'C' are more closely related to each other than
either is to species 'B'"

The question I've been driving at is whether the apparently conflicting
morphology-based and molecular-based statements are necessarily mutually
exclusive?  In other words, could they both be correct, and the real
argument is actually about what we mean by "related to"?  If we really know
for certain that the historical patterns of molecules, genes, genomes,
individual organisms, populations and taxa (in decreasing order of
"realness") are all congruent with each other in most or all cases, then my
ramblings here represent little more than a waste of bandwidth (and a waste
of my Sunday morning).

But my contention is that we really do not yet understand enough about how
to extract phylogenetic information from genetic data; and that we do not
yet understand how to reliably identify apomorphies, pleisiomorphies and
homologies from among morphological characters; and -- more fundamentally --
that we haven't even got our collective heads around what we mean by the
notion of a phylogenetic history.

But, as I have said in the past, I am optimistic that we will achieve such a
level of understanding within my professional lifetime. I fully accept that
my contentions here may amount to utter foolishness.  But I'm dubious that
anyone on this list (or on this planet) understands enough about the
relationships between organism pedigrees, genetic information, and
morphological characters to brand me a fool with meaningful certainty (on
this topic, at least) at this time.

> I've stood at the confluence of the Missouri and Mississippi rivers, and
> it's hard to point and say where the dividing line is. I've also stood at
> Lake Itasca and Yellowstone National Park, and I would bet my reputation
> that they are different places.

That's fine, but I guess I fail to see the analogy to the current topic of
discussion (let me know if you'd like me to elaborate on why I think it is
misapplied).

> >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.
>
> That's what I meant, although I tend to use the term "congruence".

O.K., then on this point, at least, our perspectives seem to
be...um...congruent...

:-)

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