Molecular phylogeny

Byron Adams bjadams at UFL.EDU
Thu Oct 9 14:30:19 CDT 2003

on 10/9/03 9:50 AM, John Grehan at jgrehan at SCIENCEBUFF.ORG wrote:

> I did not express myself well here. I am suggesting a situation where one
> can make a species tree because there are differences between he species,
> but that these relationships are all primitive retentions inherited from
> the ancestor rather than being new conditions representing the subsequent
> speciation events. Is this possible?

It certainly is possible, especially if outgroup comparison isn't employed
to polarize the characters.  In theory, as with morphological characters,
molecular characters can be polarized via outgroup comparison, and
plesiomorphies be distinguished from apomorphies.  In practice, however,
this is clouded somewhat by the saturation of changes (for nucleotides there
are only 4 states, for example), which increases precipitously when taxa
more distantly related to the ingroup are sampled for outgroup comparison.


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