Re: Phylogenetics or phenetics?

[EMAIL PROTECTED] wrote:

> In article <[EMAIL PROTECTED]>,
> John Harshman  <[EMAIL PROTECTED]> wrote:
>
> > jon rogers wrote:
> >
> > > I'd be interested to know if anyone has done a study to comparing
> > > phylogenetics with phenetics? Preferably not just on a theoretical basis,
> > > but also using practical examples?
> > Comparing on what basis? The two philosophies attempt different things. 
> > There was a considerable literature around 20 or more years ago about 
> > which philosophy produced more stable classifications, but phylogenetics 
> > won out not because it won that argument, but because phylogeny became 
> > seen as a better goal than overall similarity in its own right.
>
> It also depends on what question is being asked.  If Rogers meant the two
> approaches to classification, then they can be compared only once one has
> some agree-upon criterion, such as stability.


Agreed. Another way to put my statement was that the agreed-upon 
criterion became "accurately represents a claimed phylogenetic tree" 
rather than stability.

> On the other hand, it is common for these two words to be used to denote two
> methods of inferring phylogenies: "phylogenetic" methods being parsimony
> methods, and "phenetic" methods being distance matrix methods and sometimes
> also likelihood and Bayesian methods.  If that is the intent here, one could
> compare them by their success at recovering the true phylogeny, in cases
> such as computer simulations where one knows that.  I think that this
> terminology is a poor one, and the terms should properly be applied to
> approaches to classification.  I hope that this is what Rogers intended.


I believe that the technical meaning of "phenetic method" is "anything 
other than equally weighted, total evidence parsimony". However, 
resampling is now included in the definition of parsimony if and only if 
it's jackknifing, though I'm unsure whether the proportion sampled is 
important; it may be that only 1 - 1/e is OK, but that may have changed. 
I don't keep up with these things.