Molecular taxonomy: on way out?

[Richard Jensen]

John Grehan wrote:

>
>
> This is a claim, not something that is apparent. The idea that one has
> 'complete' data seems to reflect the pheneticist philosophy that the
> more characters one has the better the phylogeny.

I hope this was a syntactic error on your part.  Pheneticists did not claim
that more characters yielded better phylogenies.  What pheneticists did
claim was that more characters provided a better classification.  Yes,
pheneticists argued that, under certain conditions, a phenogram could be a
good approximation of a phylogenyy (as noted here before by Don Colless),
but phylogeny reconstruction was not the goal.

By the way, Steve Farris was never, to my knowledge (and I've known him for
almost 30 years) a pheneticist.  He was a numerical taxonomist (sensu lato),
but very early rejected phenetic approaches to classification.

>
>
> The choice of which aspects of phenotypic variation is not arbitrary in
> that one has to (or I should say should because oftentimes people do
> not) justify the choice and polarity. Also, it is not arbitrary in a
> cladistic sense in that only uniquely shared features have to be
> included.

There is always a degree of arbitrariness.  The systematist has to decide
which characters, of all that are available, to include.  Only if there are
specific rules that are established a priori (e.g., *every* aspect of dental
morphology that has been documented to vary within the ingroup will be
coded; *every* character for which there is general consensus on homology
between the in group and out group will be included) can you argue that
character selection is not arbitrary.  Systematists should provide
justification for the characters chosen, but that's not the same as being
non-arbitrary.  As is obvious from your comments, systematists don't agree
on which characters are valid for examining a particular group.

And, as others have pointed out, determining polarity a priori is not
necessary.  If you have a unique minimum length network for your OTUs, all
that polarity does is give you the location of the root that is consistent
with that network and your data.  It will not change the topology of the
network.

Dick J.
--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
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