distance based DNA trees

[A.P. Jason de Koning]

>ALL methods of evaluation,
> whether it be neighbor-joining, maximum parsimony, or even maximum
> likelihood include an underlying assumption that "parsimony of evolution"
> is operating. Thus both phenetic and cladistic approaches include some

Maybe that depends on what you mean by 'parsimony of evolution'.  In maximum
likelihood phylogenetics, all possible paths between observed states
(weighted by their likelihood) are considered, not just the most probable
one.  What is the underlying parsimony there?

> underlying reference to parsimony, without which just anything would be
> possible.

The probabilist view is indeed that anything is possible, though not all
things are probable.  Hence, the probabilistic approach is to calculate the
likelihood of observed character states as the sum of all possible ways of
getting there...

Cheers,
- Jason

> Brian
>
> At 09:55 15.4.2004 +1200, Rob Smissen wrote:
> >I was going to let this pass, but Curtis Clark has written it twice, and
> >I find myself in dissent.
> >
> >"Modern DNA phylogenetic
> >studies don't use distance measures. "Genetic similarity" is basically
> >too
> >crude a measure, and it's not what we are talking about here."
> >
> >I published a nucleotide substitution distance tree last year, I may do
> >it again. I very seldom find neighbour-joining trees built using an
> >appropriate substitution model differ significantly from parsimony
> >trees. Ditto for least squares or minimum evolution trees. NJ has the
> >advantage of speed. Distance trees seem to be rather more realistic in
> >estimating internal branch lengths for ancient radiations as a bonus.
> >Where they do differ, there is usually a lack of clear signal in the
> >data and neither is at all reliable. Where different tree building
> >methods do give different results there is usually a specific
> >explanation - that is the disagreement reveals or at least illustrates
> >important properties of the data. Sometimes it will then be possible to
> >argue why one method is better in the specific case - I don't think you
> >can do that generally and absolutely.
> >
> >Moreover, since I keep seeing those "we stopped the search after X days
> >because the universe was going to collapse before it finished" parsimony
> >trees in the literature, maybe an honest NJ tree would be preferable -
> >at least it is locally optimal.
> >
> >There is a very handy beta version of MEGA3 available, and PAUP4b10 has
> >numerous distance options.
> >
> >If I had the time to do all those big likelihood searches I could just
> >watch evolution happen and take notes :)
> >
> >cheers
> >Rob
> >
>
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