More on the 'cladistics' of sequences

[pierre deleporte]

A 17:30 06/06/2004 -0400, Herb Jacobson wrote:
>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
>theory.

Swofford dealt with this problem in the manual of PAUP, and Farris is said 
to have come to the same conclusion independently, as follows:
given that one can always make a mistake in choosing "the" outgroup (i.e. 
choose a taxon that is in fact a member of the ingroup at stake), it's 
preferable to take into account several putative outgroups in the analysis, 
in order to try and minimize the risk.
If they all fall into the same place on the optimal topology, there is no 
ambiguity in rooting. If not, then it cannot be said for sure which rooting 
is right or wrong, but at least it's certain that some mistake has been 
committed, and one should better enlarge the scope of the  analysis, 
enlarge the putative ingroup, and consider another series of putative 
outgroups for analysing this enlarged putative ingroup.

This notwithstanding possible improvement of the character data set, which 
of course can always happen to change the rooting of the outgroups.

Pierre


Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 66
Télécopie : 02 99 61 81 88