Michael Bayly MichaelB at TEPAPA.GOVT.NZ
Fri Jun 25 08:42:48 CDT 2004

> -----Original Message-----
> From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU]On
> Behalf Of David Orlovich
> Sent: Friday, 25 June 2004 7:16 a.m.
> Subject: Re: Characters.
> On 25/06/2004, at 12:57 AM, John Grehan wrote:
> >
> > ok I did. This is probably a consequence of my use of a PAUP program
> > from some years ago where there was a choice one could make for
> > including or exlcuing autapomorphies. I would not use them. Since no
> > one does then
> Hi John et al.,
> Excluding the autapomorphies doesn't change the tree topology anyway
> (since they always map on to the terminal branches).  You do this in
> PAUP just so the consistency index is calculated without them -
> otherwise the consistency index is inflated by characters that played
> no part in the calculation of the most parsimonious tree.
> Cheers, David.

David [G'day] and others are, of course, right that leaving autapomorphies in your matrix will have no effect on tree topology in cladistic analyses.  He is also right that you generally want to exclude autapomorphies from the calculation of CI, so as not to inflate it's value.  

Maybe this is obvious...but....when presenting morphological studies (at least), it still seems useful not to completely exclude autapomorphies from the discussion of characters.  They are still a result of the research, and maybe useful for other reasons (e.g. identification).  Also, a character that is autapomorphic in one context can be synapomorphic in another, i.e., if using terminal taxa of lower rank.  Taxa of any rank could potentially, in future, be further split taxonomically - and "hey presto" that old autapomorphy could become a ready-made synapomorphy.   

>From memory, some of this stuff was discussed in the paper:
Yeates, D.  1992.  Why remove autapomorphies?  Cladistics 8: 387-389. (someone will correct me if I'm wrong).

I'll pull my head in now...


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