distance based DNA trees

Thu Apr 15 09:55:30 CDT 2004

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
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 :)


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