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Re: Philosophies for Character Ordering
David Marjanovic (firstname.lastname@example.org) wrote:
<The alternative to "ordered multistate" is "unordered multistate" and not
"binary". Ordering isn't applicable to characters with just 2 states.>
Not quite. There are actually 5 possible state configurations:
1. binary unordered: the taxon has either state 0 OR state 1.
2. binary ordered: the taxon has either state 0, or if it has 1, is
assumed to have 0 as well.
3. multistate unordered: expansion on 1. -- this I covered in my last
post, where the cranial ornamentation of an ankylosaur skull can be
variable but potentially diagnostic and in some cases synapomorphic, as is
the pattern in the roofing bones of some amphibians, near-tetrapod "fish,"
4. mutlistate ordered: expansion on 2. -- if a taxon has state 4, it ALSO
has state 4, 3, 2, 1, and 0.
5. polymorphism: the taxon has state 0 AND state 1. This can be expanded
as a prectical experiment treating each possible polymoprhic variant as a
separate taxon, and the taxon will jump nodes frequently depending on the
number of other taxa with the same condition at the same point. LOTS of
trees in this experiment. The treatement of the taxon as a single taxon
allows that as the analysis jumps the taxon around and tests tree length,
it finds the narrowest common node at which that taxon shares with all
taxa having the variable conditions not excepting that the common
characters outweigh the autapomorphic fetaures it may share with another
group. For example, if the number of polymorphisms in taxon A is 2, and
the number of shared unique autapomorphies with taxon B is 5, it will
invariably clade with taxon B, not the narrowest common node. However, if
the number of polymorphims is 10, and it shares 5 of these with one taxon
(taxon C), or a set of closely allied taxa, and the number of shared
unique autapomorphies with taxon B is 5, it will find the most narrowest
common node that contains both taxon B and taxon C. If the other 5
polymorphisms might pertain to an outlying taxon D, taxon A will then move
back to that node given the uniqueness of those shared characters.
Ordering reduces this variability.
<It isn't supposed to be this. It's supposed to depict the simplest
hypothesis about the _evolution_ of said character associations.>
PAUP* will find the shortest trees (with the fewest steps) while all
assumptions made are being enforced. Not fewest assumptions, but with
these "in play" (as it were).
Jaime A. Headden
Little steps are often the hardest to take. We are too used to making leaps
in the face of adversity, that a simple skip is so hard to do. We should all
learn to walk soft, walk small, see the world around us rather than zoom by it.
"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)
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