chloroplast and other genes (was Lucy in Newsweek)

[Curtis Clark]

At 13:50 2004-04-03, Richard Pyle wrote:
>Yes, but a historical pattern of what?  Molecules? Genes? Genomes?
>Organisms? Populations? Taxa?

All of the above. Certainly all those things are of interest.

> > 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. Genetic recombination in sexual organisms
results in a network, not a tree. Lineage splitting makes it a tree.

>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'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.

>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".

>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.

Agreed.



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