Models, was Re: Australopithecus and orangutans

[Curtis Clark]

At 11:43 2003-05-16 +0200, B.J.Tindall wrote:
>Most tree modelling systems assume bifurcation - I don't think we can
>assume that this holds true in nature.

That's why they're called "models". :-)

>Such a system also assumes that a)
>the ancestors always become extinct

This is not a computational requirement, but rather a convention (IMO
unnecessary).

>and that b) we can always identify the
>terminal taxa.

Alas, that is the issue alluded to in other posts: gene trees are not
necessarily organism trees, and organism trees are not necessarily species
trees.

>In the case
>of organisms with a known fossil record this may not be so much of a
>problem, but the problem has become acute in the absence of a fossil record
>i.e. in the case of prokaryotes.

It's not the absence of a fossil record, it's the presence of genetic
exchange. If all organisms were strictly clonal, gene trees would be a true
reflection of higher-level trees. (I wonder--cyanobacteria have a
reputation of being sexless. Are their phylogenies cleaner than those of
other bacteria?)

>The message is caution, as with most data sets.

Absolutely. Caution should be applied as well to the tools.


--
Curtis Clark                  http://www.csupomona.edu/~jcclark/
Biological Sciences Department            Voice: +1 909 869 4062
California State Polytechnic University     FAX: +1 909 869 4078
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