Transition/transversion=?

Mark Siddall mes at zoo.toronto.edu
Thu Aug 24 22:32:58 EST 1995


In article <41hlip$du1 at mserv1.dl.ac.uk> Javier Quintero Vazquez <bnjquint at usc.es> writes:
>
>Greetings,
>
>Can anyone tell me:
>
>a.-In your opinion, the transition/transversion rate that would be used 
>in DNADIST program to the Cytochrome B sequence of fishes.

Ummm..... in the first place I would argue that you should not use distances 
as they violate triangle inequalities and assume constancy.  Second, 
estimates of TV:TS are usually between 1:2 and 1:10 I think.  If you
don't have a good way of telling... do you really think you should just pull a 
ratio out of the sky?

>
>b.-Previously, can I expect many differences between: a tree building with
>distances based methods/a tree building with parsimony/cladistic methods.
>

Yes.
The distance-generated tree will have _no_ logical basis, whereas
the parsimony-generated tree will have.  In the distance tree you will not
be able to reconstruct evolutionary changes whereas in the parsimony
tree you will.

Mark
-- 
Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062



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