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Testing Models against a tree (help)

aroger at ac.dal.ca aroger at ac.dal.ca
Thu Jul 20 15:48:14 EST 1995

Dear Phylogeny Aficianados,

I'm trying to test a hypothesis about character evolution
by using a "known" phylogenetic tree
and I'm wondering if someone might help me by suggesting
possible methods.  The problem is quite simple:

Assume the character states for a series of characters
are 1 or 0 (presence or absence of the character).
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)?

I have a few ideas-- perhaps someone can tell me if there is
anything invalid about what I'm about to say.  In model A, 1's
for all of the characters are ancestral, therefore the possession
of character state 1 cannot be synapomorphous for a clade.  Only
the possession of 0's can be synapomorphous.  Thus the phylogenetic
structure in the dataset will be largely determined by the 
possession of 0's as character states. However, under model B, 
the possession of both 1's and 0's can be synapomorphous.

Using this reasoning can the models be tested against the tree
by asking, does the allowance of 0-->1 transitions contribute
phylogenetic structure to the data?

Have methods been describedin the literature which deals
with these kinds of test?  My ultimate goal is to test whether 0-->1
transitions are likely to have occurred.

Any information would be of use to me.

Andrew Roger
aroger at ac.dal.ca

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