More on the 'cladistics' of sequences

Sun Jun 6 17:30:30 CDT 2004

In a message dated 6/4/2004 1:19:48 PM Pacific Standard Time,
rjensen at SAINTMARYS.EDU writes:

> Of course, changing the outgroup can have significant effect on
> relationships in the tree, but that's another story.

Are you certain of this?

Relationships in the study group are first determined in an unrooted tree
without character polarization. The outgroup is used only to root the unrooted
tree, and at that time the characters are polarized but the relationships in the
study group remain as they had been in the unrooted tree.

Since a clade has only one root, all outgroups should root in the same
location on the unrooted tree regardless of the outgroup chosen. It is certainly
true the the more distant an outgroup is from the study group, the more difficult
it is to establish homologies, but that is a question of application not


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