[Taxacom] Fwd: Re: base alignment

John Grehan jgrehan at sciencebuff.org
Mon Aug 28 12:56:13 CDT 2006

Thanks for the comments Pierre. My counter points are below. Also
several list members have kindly directed me to, or sent me some very
useful information and I will probably comment on these on the list

> discussions allowed me to understand that what you mean by "cladistic
> characters" is the set (or 'clique' in jargon) of completely
> characters (= homoplasy-free characters) as resulting from a previous
> compatibility analysis ('clique analysis') at a higher phylogenetic

No that is not correct. By cladistic character I mean any characters
(states) that can be shown to be unique to ingroup members. Such
character relationships within the ingroup may not be completely
compatible at all - hence the need for an analytical procedure to then
determine which cluster of putatively derived characters is best
supported (whether through parsimony or any other tree building
procedure one might use).

> adjusting your vocabulary to the current usage; hence I recommend as
> starters:
> "The Compleat Cladist" (E.O. Wiley et al.), and "Basics of cladistic
> analysis" (Diana Lipscomb), both available for free on the web.

I am happy with my vocabulary as it is. I already have the above

"cladistic" is
> never
> applied to characters (except by yourself it seems, as far as I know).

It's not my fault that others don't do this (which makes me wonder if
they are really pheneticists). But as to 'never' I might suggest this is
not correct.

hence your likely lasting difficulties for understanding
> cladistic litterature and discussing with your colleagues for
> morphological data and analyses as well.

I don't have any lasting difficulties understanding cladistic literature
or discussing with colleagues. People seem to understand my position
well enough, and visa versa. Whether or not we might agree or not is
another matter.

John Grehan

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