[Taxacom] Morphology vs Molecular

Tue Aug 18 17:50:07 CDT 2009

Pierre has a point. It is the analysis that is phenetic, not the traits. Okay, maybe I really meant analysis of molecular characters has much in common with phenetic analysis, particularly in equal weighting (excepting codon bias) to ensure no evolutionary contamination of the automatic classification."

_______________________
Richard H. Zander
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166 U.S.A.
richard.zander at mobot.org

________________________________

From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Deleporte Pierre
Sent: Tue 8/18/2009 4:01 PM
To: Taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Morphology vs Molecular

Richard,

I suggest that you reconsider this line of argument "equal weighting is phenetic" (even if "some way"...)
because it is highly confusing;
for instance, 'standard' cladistic  analysis (i.e. parsimony analysis) traditionally makes use of equal weights for all character changes,  at least for morphological characters,
while phenetics is  classically (and better) defined as "classifying on the basis of an index of overall similarity"

such a definition clearly rules out statements like "such and such characters (or data sets) are phenetic in themselves",
only the analysis of the characters may be "phenetic", while any data matrix of characters may be analysed either cladistically or phenetically, or any other way you like

("phenetic characters" is an obstinate 'Grehanian' confusion, apparently used as a rhetoric trick for discarding any imaginable molecular analysis, because molecular sequence data would be "phenetic" in themselves, you know... and molecularits ar just "counting bases", when morphologist certainly never "count" morphological characters, which are not "phenetic", by the way...    not to mention the fact that Grehanian "cladistics" mean compatibility analysis, and anything that is not compatibility analysis seems to be classed as "phenetic"...   sigh...
fortunately, nearly nobody on this list seems to follow such extraordinarily strange propositions)

so, you know quite well that I have some serious doubts about the rationale underlying "equal weighing",
but calling this "phenetics" cannot facilitate the discussion... 
we really need to share a common vocabulary - IMHO 

best,
Pierre

Richard Zander <Richard.Zander at mobot.org> a écrit :

> In one way, molecular is indeed phenetic. There is no weighting for
> phyletic importance. Well, there is one case, codon bias, in which
> selection on a pool of messenger RNA emphasizes one synonymous codon
> over another (if I have this right), but all other weighting (I
> think) is purely part of the analysis, e.g. avoiding 3rd codon
> positions because they may be over-saturated with changes. Basically
> the Dirichlet priors are all 1 in Bayesian analysis. In some cases
> certain site positions are weighted differently but I'm not sure how
> this is part of pre-weighting for phyletic importance.
>
> (Now ask me what phyletic importance is.)
>
> *****************************
> Richard H. Zander
> Voice: 314-577-0276
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166-0299 USA
> richard.zander at mobot.org
> Web sites: http://www.mobot.org/plantscience/resbot/
> and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
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>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
> Sent: Monday, August 17, 2009 7:09 PM
> To: Taxacom
> Subject: [Taxacom] Morphology vs Molecular
>
> Your counterargument is to say that molecular data is phenetic (how
> you got here is anybody´s guess) and that
> a unique and intimate knowledge of the characters (read, I have been
> doing this for years so trust me) trumps any
> amount of contradictory data (information that it not of the right kind).
>
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