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Re: 2 questions about characters



----- Original Message -----
From: "Charles Roustan" <charlesroustan@softhome.net>
Sent: Sunday, September 21, 2003 8:19 PM
Subject: 2 questions about characters (long!)

5 kB isn't long.

> Are characters with "intermediate apomorphies" the same as multistate
> characters?

Probably. I've never read about "intermediate apomorphies". :-)

> and when one code these, what is the guide one is supposed to
> follow to decide to code it as multistate or as your regular 2-faced
> character after all, any quantitative or qualitative, or whatever
character
> can be transmogrified into a 2-state one with better or worse results, or
am
> I wrong?

Well... usually, when you turn binary into multistate characters, you end up
with inapplicable codings. And few programs (I only know NONA) can actually
handle inapplicable codings. Hennig86 pretends this ability, but treats them
as "?", and PAUP* has never heard of inapplicability.

> what's the good in these multistate characters?

Well, some characters simply have more than 2 states.

> I can think of a
> couple of examples but perhaps you could enlighten me with another?

Lots of things are "(0) absent, (1) weakly developed, (2) hypertrophied" or
suchlike.

> Now, I agree, of course, is this the same as saying that everytime one
> doesn't know a particular character state, one should use a question mark,

...and exactly this is what the question mark was invented for. It means
"either 0 or 1 (or 2, 3, 4...)". There's much literature on "missing data",
why it doesn't influence a taxon's placement in a tree, and why it isn't as
much of a problem as one would think.

> and is this analogous to saying "I have no idea what this means, let's use
> another character and let's just draw a '?' here"?

What other character?

> [...]
> apparently the choice of characters is a function of how much you actually
> know about the groups you are fiddling with (how much you, the analyst,
> knows and also how much the entire scientific community knows about the
> given groups).

Of course.

> To end this, I would like to ask you for some references that help me get
a
> little better.

I can only think of the manual of PAUP*. Shall I send it to you (pdf)? In
addition (and more up-to-date), the FAQ is here:
http://paup.csit.fsu.edu/paupfaq/faq.html.