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RE: Erketu ellisoni online free access

I was referring to Weims 2006. In this paper, he offers more
hypothetical results rather than real evidence of having tested his
statements. No data matrices are presented, nor resultant analyses (he
does refer to a paper "in press"). He writes (p40): "I tested the
effects of adding 50 incomplete characters to a set of 50 characters in
the 16-taxon case using parsimony...adding the set of incomplete
characters generally INCREASES phylogenetic accuracy relative to
excluding them." Hell, in that case, let's just cut 50% from all the
characters of Wilson 2002 and call the results more accurate than Wilson
2002. But in all fairness to Weims, he clearly states that he was
addressing a particular condition, which he identifies as the
"Felsenstein Zone": "in which there are two long terminal branches
separated by a short internal branch" (p. 38, also Fig. 3 top). 

Kenneth Carpenter, Ph.D.
Curator of Lower Vertebrate Paleontology/
Chief Preparator
Department of Earth Sciences
Denver Museum of Nature & Science
2001 Colorado Blvd.
Denver, CO 80205
Phone: 303-370-6392
Fax: 303-331-6492

for PDFs of some of my publications, as well as information of the Cedar
Mountain Project: 

-----Original Message-----
From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu] On Behalf
Of Michael Mortimer
Sent: Tuesday, March 21, 2006 3:44 PM
To: dinosaur@usc.edu
Subject: RE: Erketu ellisoni online free access

Ken Carpenter wrote-

>Ah, not quite. Appendix 2 gives the coding for Erketu from the 
>published matrix of Wilson 2002. >Of 234 characters only 18! can be
coded for Erketu.
>That is 7.7% of possible characters! How can >anyone tell me that we 
>can assume to know so much from so little???? Keep in mind that a 
>>phylogenetic analysis is simply a form of statistics. Even Wiens' 
>article notes a decrease in reliability >of phylogenetic results when 
>75% or more of the data is unknown (his Fig 2). Here 92% is

In case you were referring to figure 2 of Wiens' 2003 paper, it actually
means something else.  It shows that adding a set of 50 new characters
to a 50 character analysis is beneficial unless those new characters are
unknown in 75% or more of the taxa.  And even then, they're not harmful
to add.  So it's about adding incomplete characters to analyses (like
integumentary or eggshell characters in Mesozoic dinosaur analyses), not
incomplete taxa.

What you want to refer to is figure 1, where the affect of incomplete
taxa (like Erketu) is analyzed.  Wiens notes- "Given enough characters
in the analysis, it is possible to have extremely accurate resolution
when including taxa that are only 5% complete and that have nearly 2000
missing data cells each (Fig. 1). Clearly, the amount of missing data
itself is not the actual problem. As long as enough characters are
sampled in the incomplete taxa to accurately place them on the tree,
then the amount of missing data seems to have little impact."
Wiens' later (2006) paper has equivalent graphs to figure 1 for a 200
character analysis.  In particular, figure 2b of Wiens (2006) is
relevant*, being a parsimony analysis where the characters taxa lack
data for vary among those taxa (as in sauropod analyses where some taxa
are only known from skulls, some lack skulls entirely, etc.).  It shows
that even when _half_ the taxa have 90% of their character states
unknown, the results are still over 50% accurate.  Of course, every
other taxon in Wilson's analysis is more complete than Erketu, and the
average amount of unknown data is 45%, even taking Erketu into account.
So the accuracy should be >90%, according to Wiens' graph.

Wiens' analyses do show that we need to use more characters in our
morphological analyses however.  Are 2000 characters too much to ask for
in a sauropod analysis?  I don't think so.  And if we can reach that
point, we can have 100% accuracy even if our matrix is 75% incomplete.

* So if you were referring to figure 2 of Wiens 2006, and not Wiens
2003,, ignore my first paragraph.

Mickey Mortimer