Re: PhyloCode Discussion: Crowns, Panstems, and their Correspondence to each oth

[Mickey Mortimer <Mickey_Mortimer111@msn.com>]

David Marjanovic wrote-

> (http://www.palaeos.com/Vertebrates/Units/430Mammalia/430.400.html
expresses
> discontent with Luo et al. 2002, though.)

But their example showing why they believe Luo et al. is flawed is
incorrect.  They state-

"A substantial number of dental characters are included which are not
applicable to animals without certain minimal dental equipment: trigon,
protocone, or what have you.  The only correct way to score these, or any
other, characters is to begin with the outgroup condition as plesiomorphic.
If that means "not applicable" is scored as zero, that's perfectly  OK.
What is not permissible is to score "not applicable" as if it were missing
data.  This is what Luo et al. do."

However, the Luo et al. did the right thing.  By coding some trigon
characters as 0 in taxa without a trigon, you're making a subjective
judgement about character polarity.  Namely, that whatever trigon state you
choose to be 0 is primitive, and thus easily derived from the taxa lacking
trigons.  If they don't have a trigon, they can't have either state of a
trigon character.  And you can't make an extra state 0 for taxa without
trigons (the outgroup), leaving states 1 and 2 for the different trigon
morphologies.  This would end up weighting the presence of a trigon.
It would be like deciding the code a fish as having brown hair for the
character "hair - color - brown (0); black (1)".  The proper method is to
code it as inapplicable.

Mickey Mortimer