[Taxacom] real molecular data

Hovenkamp, P. (Peter) Hovenkamp at nhn.leidenuniv.nl
Fri Nov 14 02:25:16 CST 2008


John,

If you ever want to convince others of your point of view, you can save
yourself the trouble of scanning thousands of positions until your eyes
start to twitch. The only result of this appears to be that you point
out how few apomorphies there are that are completely free of homoplasy.
Dismisssing characters when they show only a single instance of
homoplasy has been briefly in fashion in the late 70's-early 80's - it
was called compatibility analysis then, and was thoroughly discredited
under the name of clique analysis. 

Merits of the method aside - no-one is going to be convinced of your
point of view if that is all you can present as support for it. 


Peter Hovenkamp
Nationaal Herbarium Nederland, Leiden branch
www.nationaalherbarium.nl  

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
> Sent: Thursday, November 13, 2008 6:39 PM
> To: TAXACOM
> Cc: Fetzner, Jim; Colin Groves
> Subject: [Taxacom] real molecular data
> 
> OK - just to prove I am nuts, I scanned every one of 21,507 sequence
> positions for coding data in the Prasad et al 2008 study 
> (Confirming the
> phylogeny of mammals by use of large comparative sequence 
> data sets Mol.
> Biol. Evol. 25: 1795-1808). The coding sequences produced (by 
> parsimony
> analysis) a human-chimpanzee clade followed by gorilla and orangutan.
> 
>  
> 
> I found the following (although I admit in advance I may have missed
> some. I had a twitch in one eye for a while)
> 
>  
> 
> Human-chimp - 2 apomorphic bases
> 
> Human gorilla - 1 apomorphic base
> 
> Human-African ape -  20 apomorphic bases
> 
> Chimp-gorilla - 1 apomorphic base
> 
>  
> 
> These apomorphies were defined as being absent from all other 
> primates -
> in this case only 12 species. In morphology this limited 
> sampling would
> be usually recognized cladistically as an absurdly small outgroup
> representation. The outgroup taxa in this case were:
> 
>  
> 
> 1 gibbon
> 
> 1 colobus monkey
> 
> 1 vervet monkey
> 
> 1 baboon
> 
> 1 macaque
> 
> 1 duski titi
> 
> 1 owl monkey
> 
> 1 squirrel monkey
> 
> 1 marmoset
> 
> 1 galago
> 
> 1 mouse lemur 
> 
> 1 lemur.
> 
>  
> 
> The best I think that may be said of the molecular evidence supporting
> the human-chimpanzee relationship is that it is 'overwhelming' if one
> ignores the non-cladistic nature of alignment, and the small outgroup
> sampling that create apomorphies as an artifact of small 
> outgroup sample
> size. For example, at site 14,466 there humans and African 
> apes share A
> and that would have been an apomorphy if it were not for the inclusion
> of that one gibbon where it also turned up.
> 
>  
> 
> So my conclusion is that the molecular claims of proving the
> human-chimpanzee relationship is more propaganda than 
> science, and more
> phenetics than cladistics.
> 
>  
> 
> I rest my case (for now).
> 
>  
> 
> John Grehan
> 
>  
> 
> Dr. John R. Grehan
> 
> Director of Science
> 
> Buffalo Museum of Science1020 Humboldt Parkway
> 
> Buffalo, NY 14211-1193
> 
> email: jgrehan at sciencebuff.org
> 
> Phone: (716) 896-5200 ext 372
> 
>  
> 
> Panbiogeography
> 
> http://www.sciencebuff.org/biogeography_and_evolutionary_biology.php
> 
> Ghost moth research
> 
> http://www.sciencebuff.org/systematics_and_evolution_of_hepialdiae.php
> 
> Human evolution and the great apes
> 
> http://www.sciencebuff.org/human_origin_and_the_great_apes.php
> 
>  
> 
>  
> 
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