More on the 'cladistics' of sequences

[HJJACOBSON at AOL.COM]

In a message dated 6/7/2004 7:47:50 AM Pacific Standard Time,
pierre.deleporte at UNIV-RENNES1.FR writes:

> 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.


I certainly agree with the above. Had I realized that this is what was meant
in the note that I first responded to, I would never have responded. Of course
different putative outgroups may change the ingroup relationships because
some are in error. I interpreted outgroup in the first communication as outgroup
and not putative outgroup. That's not a criticism of anyone writing, just a
comprehension problem on my part.

It does bring up the point touch on by Zdenek Skala: If taxa are not in the
outgroup are they then in the ingroup, or is there a limbo out there? For
example if I find that taxa A,B,&C used as outgroups each changes the ingroup
topology but find that C,D,&E produce the same ingroup topology, does that mean
that A,B&C are really part of the ingroup? Whether building a tree this way is
phenetic or not is an idea that I will have to think about.

Herb