[Taxacom] Morphology vs Molecular

Thu Aug 20 08:36:18 CDT 2009

I find it interesting that it is recognized that some techniques failed. I am sorry if it seems that I am cherry picking the failed techniques. I am happy to acknowledge all failed techniques.

And your acknowledgement of how one interprets phenetic analysis not being clear-cut does seem to pertain to my arguments. If its not clear cut then there is a problem.

Yes, the key is comparison of homologous structures. In DNA sequences this seems to be determined by position, but recognizing the same position between species and higher taxa appears to have been problematic - and in my opinion it is one possibility by which erroneous similarity is retained or introduced in the analysis.

A undestand the principle that a synapomorphy is determined by the results of the analysis, but my particualr view is that the data being analyuzed is limited to those similarities that are shared derived for the group being analyzed. In morphology the derived condition can be articulated and justified for each indivudual character. In sequence analyses this appears to be more problematic - in my opinion.

More data may or may not help. In some case one might still end up with a 50:50 split between characters with 5, 100, or a million characters. 

What is perhaps remarkable for the human-orangtuan example is that not only are there are as many morphological synapomorphies as found so far - at least 28, and may be at least 45, but that in molecular approaches this is not supported (interestingly, in some sequences I have scanned there are clusters for human-chimp, human-gorilla, human-African ape, but none or almost so for human-orangutan).

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
> The point is that you can´t cherrypick the failed techniques to serve your
> purpose. In particular your insistence on using the word similarity; rings
> hollow by now. As Pierre correctly pointed out the analysis can be
> phenetic, of course how you interpret this is not clear-cut. Sequence
> alignment of genes with large indels is the closest you get to this and
> that is why they are frequently culled. The key is that what you compare
> are at least homologous structures. If they happen to be synapomorphies or
> not that depends on the results of your analysis.
> 
> Neither counting bases nor setae nor measuring the relative sizes of
> foramens is going to give you a ticket to the truth, but you may get
> closer to it the more data you throw at it.
> 
> 
> > Date: Wed, 19 Aug 2009 17:32:56 -0400
> > From: jgrehan at sciencebuff.org
> > To: taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] Morphology vs Molecular
> >
> > Yes hindsight may be 20:20 - but the point here is that is what
> molecular hindsight concluded.
> >
> > John Grehan
> >
> > > -----Original Message-----
> > > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> > > bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
> > > Sent: Wednesday, August 19, 2009 5:19 PM
> > > To: Taxacom
> > > Subject: Re: [Taxacom] Morphology vs Molecular
> > >
> > >
> > > And phrenology didn´t yield the desired results either. Hindsight is
> > > 20:20.
> > >
> > > > Date: Wed, 19 Aug 2009 16:57:04 -0400
> > > > From: jgrehan at sciencebuff.org
> > > > To: Taxacom at mailman.nhm.ku.edu
> > > > Subject: Re: [Taxacom] Morphology vs Molecular
> > > >
> > > > Pierre is correct that counting occurs in morphology as well as
> > > molecules, but it's not a matter of just counting bases, but whether
> > > counting bases will necessarily give the correct phylogeny. This has
> > > already been recognized among molecular systematists who have
> recognized
> > > that some molecular techniques, such as DNA hybridization, are indeed
> > > measures of overall similarity that may give erroneous results due to
> the
> > > effects of shared primitive retention.
> > > >
> > > > John Grehan (the obstinate)
> > > >
> > > > Perhaps that will go on my gravestone.
> > > >
> > > > > -----Original Message-----
> > > > > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> > > > > bounces at mailman.nhm.ku.edu] On Behalf Of Deleporte Pierre
> > > > > Sent: Tuesday, August 18, 2009 5:02 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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