Re: Transformational and taxic approaches to character coding [was Re: Philosophies for Character Ordering]

[David Marjanovic <david.marjanovic@gmx.at>]

I'm among those who don't like getting a cc of everything, because this
means getting each e-mail twice within the same minute.

> Note that I specifically
> code for the presence of cotylar caudals as a similarity among these
> organisms, even though the picky anatomical details (i.e., which end is
> cotylar) are different.

Is it really a picky detail which end is cotylar?

> 1. Caudal vertebrae: 0) amphicoelous, 1) with condylar articulations on
some
> vertebrae
>         If the condylar articulations extended throughout the column in
some
> taxa, I would add a third state for that, and order it because the states
> CLEARLY overlap.
> 2. Caudal vertebrae with condylar articulations: 0) on proximal face of
> centrum, 1) on distal face of centrum.
>         This character must be scored as unknown for taxa that have
> character 1, state 0.

Actually it must be coded as inapplicable for those that have 1(0). PAUP* is
incapable of this, so "unknown" would be the method of choice -- with some
amount of bellyache. NONA is able to deal with inapplicable codings.
Hennig86 claims to be, but just treats them as unknown...

> Also note that I am NOT subscribing to the convention
> that the ancestral state must be coded as 0.

In PAUP* at least, this doesn't matter, because PAUP* makes unrooted trees
that are a posteriori rooted with the outgroup (if you don't tell it
something else).

> An alternate coding:
> 1. Caudal vertebrae: 0) amphicoelous, 1) with condylar articulations
> 2. Distal articulation: 0) cotylar, 1) condylar
> 3. Distal articulation: 0) cotylar, 1) condylar

Why not:

1. Proximal articulation: (0) cotylar, (1) flat, (2) condylar
2. Distal articulation: (0) cotylar, (1) flat, (2) condylar

This allows for biconvex (22), amphiplatyan (11) and amphicoelous (00)
vertebrae as well as procoelous (02) and opisthocoelous (20) ones. These two
characters are (almost?) independent, because only (01) and (10) don't occur
in reality (or do they?), and they're certainly logically independent. -- 
This way of coding does however bring up the problem of whether to order
these characters. And here we should really know something about their
developmentary genetics.

> 1. Caudal vertebrae: 0) procoelous, 1) amphicoelous, 2) opisthocoelous
> [ORDERED]

...(3) biconvex, (4) amphiplatyan [FANCY STEP MATRIX]? Sure, if you're
lucky, you don't have taxa with those morphologies in your matrix, but...

> You can also selectively unorder this character to
> see if the relevant parts of the analysis are sensitive to that
> "assumption." In my limited experience, such sensitivity is rare.

But to do this test usually increases the impressiveness factor of your
results (by showing how robust they are), and therefore perhaps the impact
factor of your paper, too. =8-)