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Re: MacClade vs. PAUP

David Peters (davidrpeters@earthlink.net) wrote:

<What does it mean when MacClade (through human manipulation) comes up
with a tree that is two steps shorter than the best one PAUP can produce?>

  Two different algorithms used to compare the same dataset, they are not
combined in the same way. PAUP* seeks to find data by particular
algorithms for merely shortening the tree, regardless of reversals etc.
MaClade will actually test shortening via reversals, and allow you to seek
minimal reversals with shortest lengths, but doesn't test for things PAUP*
does. It seems recommended by practice at least by Tom Holtz' work to run
the trees in PAUP*, then pass the dataset through MacClade to gain a sense
of the transformation of characters.

  Note: Evolution does NOT always take the shortest route, and in fact
there's only anecdotal consideration that it does. Rather, selection finds
the most equitable circumstances to preserve a species given it's genes
and the environment. This is just one manner in which evolution is
theorized to proceed. Thus, shortest trees are not always the preferred
goal of the analysis, and PAUP* allows you to look at trees of ANY length
for the purpose of a concensus, constrain topologies and rerun, things
which MacClade cannot.

  Note the Second: The output is only as good as the input. If one is
assessing the whole of Diapsida or Sauropsida, one had better have more
than 500 characters, since there are a LOT of animals being assessed here.
It is also wise to avoid suprageneric clades, but to use species as
specifiers, and list all which specimens were coded from in an appendix or
table, for the sake of reference. This is my one major gripe with Rauhut's
recent (and thought provoking) analyses.


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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