[Taxacom] Morphology vs Molecular

[John Grehan]

I will have to admit that I am not familiar with the details of on how measures of overall similarity are chosen (since I have not endevoured to carry out that kind of analysis). The problem of overall similarity remains, in my mind, a key problem for sequence analyses. The argument goes that techniques such as DNA hybridization are now recognized as phenetic in that they measure overall similarity that includes both derived and retained character states. Sequence analyses are supposed to be cladistic, but it seems that this is also problematic. 

Any molecular analysis that begins with alignment is invoking a measure of overall similarity that minimizes a theorized cost in the number of gaps and substitutions so that any subsequent analysis is based on that phenetic, rather than cladistic, foundation. Other clustering methods seem to produce a tree from which 'derived' states are supposed to be first identified, and distance measures in particular seem to be just measures of overall similarity. Perhaps I am wrong about this, but there has been no empirically based argument by molecular systematists to show that the molecular data is not phenetic, but cladistic in the same sense as in morphology.  

Some analyses have attempted to introduce a 'cladistic' aspect through outgroup comparison, but this is often woefully inadequate with the outgroup scope being limited to a few 'representative' taxa (often in just the immediate sistergroup) that assumes that the sequence site will be the same in all other members of the outgroup. In our hominid analysis we used a broad outgroup comprised of lesser apes (11 species) and at least all OW monkeys (couple of hundred species). However, in reality some features we included were not documented for all species, so there is that shared weakness (although we do document exactly which taxa are represented). 

The 'best' characters are those for which all outgroup taxa are known. A good example is the single incisive foramen of humans and orangutans. Only the great apes have an incisive foramen (other primates have fenestrae) so this is a definitive apomorphy for humans and orangutans.

Of course the ideal step would be to get adequate documentation, but that takes $. The only realistic opportunity here is NSF, but that's basically a popularity contest and if the hostility towards the morphology evident on this list (which is mild indeed compared to primate biologists) is reflected in the reviewer pool, then one can anticipate how productive that attempt would be.

John Grehan


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of bti at dsmz.de
> Sent: Thursday, August 20, 2009 1:18 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Morphology vs Molecular
> 
> Thank you for clarifying your usage. I stand corrected if I
> interpreted your usage wrong. One point that has had be curious is
> what are the consequences of "overall similarity" - does this mean
> that one must aalways generate a mathematical similarity value or can
> one score this based on an the "overall picture". The "classical"
> pheneticists tended to generate similarity values, but I am not sure
> if this always has to be the case. Just a thought.
> 
> Brian
> 
> Quoting John Grehan <jgrehan at sciencebuff.org>:
> 
> >> bounces at mailman.nhm.ku.edu] On Behalf Of bti at dsmz.de
> >> It is not just John Grehan who uses terms in a more than "derived"
> >> fashion phenetic = phenotype and cladistic = molecular.
> >
> > Correction - I use phenetic to refer to overall similarity, whether in
> > morphology or molecules and cladistics to refer to analysis of the
> > distribution of derived character states shared between various taxa of
> > an ingroup.
> >
> > 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 with that I could concur.
> >
> > If you consult many of the
> >> taxonomic papers in prokaryote research one finds three data sets -
> >> genetic, phenotypic and phylogenetic.
> >
> > Which would be confusing indeed.
> >
> > John Grehan
> >
> >
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