[Taxacom] Morphology vs Molecular

[bti at dsmz.de]

Interestingly, Richard posted a link to a paper a couple of weeks ago  
(American Journal of Botany 90(9): 1263?1270. 2003) in which the  
author refers to "phenetic cladistics" (i.e. cladistic evaluation  
based on phenotypic = morphological data) and "molecular cladistics".  
It is not just John Grehan who uses terms in a more than "derived"  
fashion phenetic = phenotype and cladistic = molecular. Given the fact  
that the original definition of phenetic initially centred on the  
phenotpye but indicated that it could include genetic characters "as  
they become available" and Hennig's "phylogenetic systematics" =  
cladistics started off using morphology half the debate centres on the  
how terms are being used by different scientists and how their  
concepts attached to those terms differ - sounds a bit like  
nomenclature and taxonomic concepts. If you consult many of the  
taxonomic papers in prokaryote research one finds three data sets -  
genetic, phenotypic and phylogenetic.

Brian

Quoting Richard Zander <Richard.Zander at mobot.org>:

> 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
>> Non-post deliveries to:
>> Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110
>> *****************************
>>
>>
>> -----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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