chloroplast and other genes (was Lucy in Newsweek)

[Curtis Clark]

At 13:14 2004-04-04, Richard Pyle wrote:
>How confident are you that all these patterns are going to be exactly the
>same?

I'm completely confident that they will *not* be exactly the same.
Evolution isn't that simplistic. (And to paraphrase a colleague, if working
out evolutionary history were easy, it would already be done.)

>How often do publications dealing with phylogenetic patterns identify
>which one their evidence pertains to?

Perhaps not nearly often enough. :-)


> > > > 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?

Of course.

>Embryonic
>development and subsequent organismal growth does indeed represent the
>assemblage of matter -- doesn't it?

Yes. (But I'm not sure why this is important to the issue at hand.)

>Over the course of an organism's life,
>entropy is always at play (especially after an organism dies) -- correct?

Even before, in the other direction.

>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.

I think so...

> > 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????

None of the phenomena you mention will give rise to a tree.
Lineage-splitting is the additional requirement, and I and many others
associate lineage-splitting with speciation. The evidence is IMO
overwhelming that speciation is not completely dictated by recombination in
populations (certainly it would be folly to assume that geological
vicariance events resulted from gene flow).

>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".

That's not the only way to look at it. You could talk about population
lineages. You could talk about coalescence of gene trees. You could talk
about it as a hierarchy of apomorphies. My point is that none of those
things solely (or even perhaps jointly) *determine* evolutionary history;
they are simply different ways of looking at the pattern.

>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.

I suggest that the shorthand version is more accurate, because it makes
fewer assumptions.

And I object to your equating "real" and "discrete". I am convinced that I
am real, and I suspect the same of you, but I'd be hard-pressed to
demonstrate that I were discrete. The requirement of discreteness is IMO
one of those Aristotelean leftovers that hinders modern science. Certainly
the particle physicists have gotten over it.

>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".

I claim this as an *outcome* of lineage-splitting.

>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".

This is meaningless as stated, because it makes no provision for
autapomorphy or saturation, which could decrease sequence similarity
between closest relatives (however you want to measure it). That's why
"mere" similarity coefficients don't work for phylogenetic studies of DNA.

>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".

Um, I think you are using "congruent" in a sense that I don't understand.
Do you mean that "A" and "B" share more apomorphies?

>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'd say no, but because of technicalities.

>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).

My ramblings are based on the idea that we don't know that for certain, but
that we have well-established theories of the ways that "traits" (genetic
or morphological) can be transferred longitudinally or laterally. One
approach to non-congruence is to throw up our hands and say "It's too
complicated, so I'm going to stuck with my 'expert taxonomic opinion'."
Another is to postulate unknown forces at work. I maintain that the best is
to analyze the data in the context of accepted mechanisms and see whether
we can make any sense of it.

>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.

And this is different (in the context of the history of science) how?

>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 agree (although I'd be surprised if it happened within mine).

>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'm certainly not going to brand you a fool; yours are among the
best-thought-out posts on the list. It always surprises me when you write
something that I regard as a "mistake". :-)

> > 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).

It's a metaphor about the difference between discreteness and reality.


--
Curtis Clark                  http://www.csupomona.edu/~jcclark/
Web Coordinator, Cal Poly Pomona                 +1 909 979 6371
Professor, Biological Sciences                   +1 909 869 4062