Testing Models against a tree (help)

aroger at ac.dal.ca aroger at ac.dal.ca
Tue Jul 25 19:32:28 EST 1995

In article <3umno4$fb9 at nntp3.u.washington.edu>, joe at evolution.genetics.washington.edu (Joe Felsenstein) writes:
> In article <1995Jul20.174815.39942 at ac.dal.ca>,  <aroger at ac.dal.ca> wrote:
>>I have two alternative models of character state
>>change that I wish to test
>>Model A:
>>1-->0 (where 1 is ancestral for all characters)
>>Model B:
>>1-->0 and 0-->1 (where 0 is ancestral for all characters)
>>I can assume a tree which accurately describes the organismal
>>relationships, what I wish to do is ask: which model better
>>fits the data given the tree?  How should I do this using simple 
>>methods (for instance using a parsimony framework)?
> Inevitably, if one uses parsimony, model B will fit better (or at any rate no
> worse) than model A.  That is because it allows all the events in model A.
> One could use the Templeton "paired sites test" as to whether the sum of
> changes in model A is significantly worse than in model B.

Is it really inevitable if I fix the ancestral states (0 for all
characters for model B, whereas 1 is fixed for all characters
under model A)?  I can see your point if there were no conditions
imposed upon the ancestral states.

Is the Templeton paired sites test the same as the widely discussed
"Templeton test" of whether one tree is significantly better than another
given the data?  If not could you suggest a reference that I might
look to?

I have another test in mind.  Perhaps someone could tell me
if it is sound.

Under model A I could construct a tree from the data and measure the
tree to tree distance from the "known" tree of the organisms.  I could
then construct a tree under model B from the data and derive the
tree to tree distance of this tree compared to the known tree.  If
model B yields a tree closer to the true tree (smaller tree to tree
distance) then I suggest that this model is more realistic.  The
only problem I can see is whether the tree under model B is 
significantly closer to the true tree than the tree under model A--
ie I need a statistic attached to the tree to tree distance measures.

Does this sound reasonable?

Thanks in advance,
Andrew Roger
aroger at ac.dal.ca

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