chloroplast and other genes (was Lucy in Newsweek)

Richard Pyle deepreef at BISHOPMUSEUM.ORG
Sat Apr 3 00:17:34 CST 2004

> My impression is that some 10 years ago we were given the impression that
> once complete genomes were available we would have all the answers.

I commented on this issue in a recent post, and was a bit (pleasantly)
surprised that it sparked very little protest.  My contention was that the
best *information* for inferring phylogenies is in the genome.  After all,
everything in the morphology that represents phylogenetically informative
evidence is, essentially by definition, also in the genome (and presumably
more "cleanly" represented therein). The problem, of course, is that we
still don't really know how to access that genomic information yet.

I also predicted that our technological ability to obtain whole genomes
cheaply and quickly will arrive somewhat before our ability to reliably
extract the phylogenetically useful information (e.g., we already know the
whole human genome, yet we have barely begun to understand how to interpret
the information for constructing a human being from it).  I suspect that
when we do understand how to extract the information, we will come to
realize that the WHOLE genome is not really needed to be able to infer a
phylogeny that approaches the "confidence asymptote" (i.e., the greatest
confidence in evolutionary affinities that can possibly be achieved).  So,
in a sense, I agree with the inference intended by the comment above: that
simply having access to complete genomes would not provide all us with all
of the answers ('though I'm not sure I've ever met anyone who actually
believed that it would -- even 10 years ago).

However, I guess my underlying point is that our current efforts to
reconstruct phylogenies, and our arguments about what approaches are most
"reliable" etc., will probably seem rather quaint a few decades hence.
That's not to say that they're a waste of time (we have to figure it out
somehow). But the level of passion that sometimes lies behind these debates
seems a bit out of place and unwarranted, in that context.

On a final note, we often like to think of "species" as being discrete
entities; but of course they are not.  And because they are not (i.e.,
because they are "fuzzy"), they do not have a discrete phylogeny.  One could
argue that individual organisms have a discrete phylogeny (pedigree), but
when you really dissect it, individual organisms aren't perfectly discrete
entities either -- they start out as a union of two cells, and continuously
change throughout their entire life spans.  I wonder how many molecules
contained in the sperm and the egg are still with the organism when it
eventually dies (also, I've heard numerous times -- but have yet to
satisfactorily corroborate -- that something over 90% of the cells in a
human body are non-human).  So even individual organisms aren't really
discrete entities.  One could say that a genome is the discrete phylogenetic
entity; but even there we have a change between the mix of genetic material
contained in the gametes that started the organism, compared with what is
contained in any given gamete cell produced by that organism.  So we come
back to the Dawkins-esque perspective that it's the genes themselves that
are the phylogenetic entities.  I think it was Curtis Clark who said
"lateral transfer is very much less common that longitudinal
(generation-to-generation) transfer."  Very true...but when you allow for
evolutionary time scales, a tiny fraction of lateral transfer could
potentially compound over time and end up with a meaningful incongruency
between what we like to think of as an unbroken lineage of organisms, and
the composition of the genetic material they harbor.

Goodness!  Look at the time.  I was going to follow on this logic down
through molecules, atoms, subatomic particles, and superstrings....but I get
the sense that such a discourse would be of very little benefit to most
folks -- including me.


Richard L. Pyle, PhD
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at

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