More on the 'cladistics' of sequences

[rjensen at SAINTMARYS.EDU]

 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?

Yes.

>
> 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.

If one is fortunate enough to have a situation in which alternate outgroups all root the tree at the same point, then you are right.  But, changing ourgroups can change the location of the root, and this has major implications for identifying major clades.

>
> 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
> theory.

Each "subclade" on the unrooted network has a single root; but, a priori, you don't know where to root the unrooted network. Rooting does not alter the monophyly of the ingroup, but it can alter interpretations of what constitute clades within the ingroup.

Here is an unrooted tree:          A          C
                                                 \____/
                                                 /       \
                                               B         D

There are five internodes and rooting at each one produces a different tree, hence, a different set of hypotheses about character evolution (i.e., homologies and homoplasies)

Dick