Molecular taxonomy: on way out?

[Derek Sikes]

John,


>> Only in phenetic analyses can a plesiomorphy 'support' a
>> group - but modern molecular phylogenetics are not phenetic.
>>
>
On 18-Jul-05, at 11:13 AM, John Grehan wrote:

> They are if they treat plesiomorphies as synapomorphies as an artifact
> of the analysis.

No a phenetic analysis can support two clades, one with the
plesiomorphic state and one with the alternate apomorphic state of
the same character since the very idea of derived and primitive (and
states for that matter) is meaningless in a phenetic (ie distance)
analysis.

For a very nice example of how this can happen see pages 68-73 of
Diana Lipscomb's 1998 BASIC CLADISTIC ANALYSIS at

http://www.gwu.edu/~clade/faculty/lipscomb/Cladistics.pdf

which shows a phenogram that has two "clades" supported by
plesiomorphies which in the example are not marked on the phenogram
because they are not derived states.

Mistaking a plesiomorphy for an apomorphy is a mistake not of the
method but an error that can happen to a traditional morphologist as
easily as it can happen in a molecular analysis (and I've seen plenty
of poorly done 'traditional" morphological analyses as judged by well-
done modern morphological analyses). Any phylogenetic analyses may
sometimes make this mistake but this does not make the analysis
phenetic.

The point is that whatever state is found to be plesiomorphic,
whether that is the truth or not, cannot be used to support groups in
a phylogenetic analysis - such states are ignored. Yes, ignoring them
may be a mistake because they may actually be apomorphies, but,
again, making this mistake does not make the analysis a phenetic
analysis - because, of course, you must admit that traditional
morphologists sometimes make this mistake too! (and doing so doesn't
suddenly change their cladistic analysis to a phenetic one!)

If both molecular and morphological methods sometimes produce
erroneous character state polarizations, which we know can happen,
then you cannot claim that one method is inferior (ie suffers an
artifact) to the other for this reason. You may try to argue that one
method is more likely to make this mistake more often than the other
- but to make this argument you will need, I'm afraid, some evidence.

Yours,
Derek
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Derek S. Sikes, Assistant Professor
Division of Zoology
Department of Biological Sciences
University of Calgary
2500 University Drive NW
Calgary, Alberta, Canada, T2N 1N4

dsikes at ucalgary.ca
http://homepages.ucalgary.ca/~dsikes/sikes_lab.htm

phone: 403-210-9819
FAX:  403-289-9311

"Remember that Truth alone is the matter you are in Search after; and
if you have been mistaken, let no Vanity reduce you to persist in
your mistake." Henry Baker, London, 1785

Entomological Society of Alberta:
http://www.biology.ualberta.ca/courses.hp/esa/esa.htm
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