[Taxacom] molecular nonsense?

Alan DAvid Forrest aforrest at rjb.csic.es
Thu Nov 6 09:25:34 CST 2008


Please do not allow all researchers who use molecular data to address 
hypotheses to be tarred with the brush of poor quality science. There 
are many examples of the latter - I am aware of papers rejected due to 
poor quality science, only for them to be published soon afterwards 
despite any concerns. This does not invalidate molecular data in general 
terms.
.
Molecular data (when of high quality and analysed appropriately) can 
reveal additional insights, as the mode of inheritance of homologous 
nucleotides is well understood, which is not always the case for 
morphological character states: our knowkledge of the inheritance of the 
latter is patchy and does not conform to any over-riding rules. For 
example, in the following paper: Grehan (2001) Biogeography and 
evolution of the Galapagos: integration of the biological and geological 
evidence. Biol. J. Linn. Soc. 74, 267-287, a biogeographic track is 
analysed in the Galapagos, using as an example the plant genera Galvezia 
and Gambelia, which are assumed to be sister genera based upon a 
morphological taxonomic monograph and a study of the genera using 
allozymes - the absence of a tribal analysis to establish sister genus 
status is somewhat lacking in the literature. Our own (as yet 
unpublished) work has used four genes (both plastid and nuclear) 
alongside other biological and morphological data (including outgroups 
from across the included tribe, all other tribes in the family, and 
several taxa from related but increasingly distant families) to show 
that these 2 genera are completely unrelated. The key here is the 
diversity of data used, and the appropriate sampling and analyses which 
was not apparent from previous publications.

In this case molecular data are just another form of data. Incongruence 
between data types requires analysis of what causes the incongruence, 
not rejection of one data in favour of another based on a priori 
preferences.

Remember, the most important thing in science is to get some good 
publications as this is how you obtain employment. The quality of the 
science underlying those publications we can worry about at a later 
date. Chimps and humans are a hot topic.

AD Forrest









John Grehan escribió:
> Ebersberger et al (2007) Mapping human genetic ancestry. Mol. Biol.
> Evol. 24: 2266-2276
>
>  
>
> I am grateful for one list member sending me the above work as "rather
> relevant for your questioning of the (human, chimp) relationship"
>
>  
>
> It certainly is, and illustrates what I see as continuing illusion of
> the putative chimpanzee-human clade. The paper uses a likelihood
> approach (correct me if I am wrong, but I understand that this approach
> sort of models what the true tree is supposed to be in the first place)
> to "identify those sequence trees that significantly reject chimpanzees
> as our closest relatives, that is, are incongruent with the species
> tree". There you have it, anything that does not fit must be wrong. The
> authors begin with the human-chimpanzee assumption and interpret
> everything from there. This seems to me a continuance of the molecular
> propaganda machine.
>
>  
>
> Cladistically the taxonomic sampling is nonsense. To evaluate
> relationships of humans and great apes the outgroup is just one monkey
> species! The authors also admit that they have no information on the
> quality of the individual aligned sequence reads! Amazing! Is this the
> standard of systematic quality for molecular analyses? Imagine the
> response if a morphologists tries to say that they had no information on
> the quality of morphological homologies! The authors then proceed to
> invent the quality through a series of computational manipulations to
> somehow make the data good. They end up with 30,112 multiple sequence
> alignments that are available upon request (I will be requesting).
>
>  
>
> The authors "re-estimate the splitting times for the human and great ape
> lineages." Hmmm - wonder why they have to do that. If molecules are
> supposed to give the right answer, then why revisit what has already
> been determined? On p. 2274 the authors node that "it is still unclear
> when in our evolutionary history we split from the ancestral species
> shared with the chimpanzees. Hmmm - maybe because the theory is wrong in
> the first place!
>
>  
>
> "Particularly puzzling in this context is the apparent discrepancy
> between the dating of this split based on genetic evidences and the age
> of fossils." Well, their answer in short is that the fossil record is
> wrong because morphology is wrong! They state "The unequivocal
> assignment of fossil remains to a species more closely related to humans
> than to chimpanzees based on the presence of certain human-specific
> apomorphies should, therefore, be taken with a grain of salt"!!!!! This
> authoritative statement mirrors what Jeff and I have been saying for
> some time - if only DNA can be relied upon to give the right answer then
> the entire fossil record is scientifically meaningless, and now some
> molecular experts are saying the same thing! All you morphological
> systematists - you are going to be out of job.
>
>  
>
> Anyway, they note that the "current interpretation of the fossil record
> argues for the presence of hominids already at 5.8 MYBP" and possibly
> earlier. The molecular study manages to come up with the 'right' answer
> divergence estimate of 5.7 Ma (2270) Believe it or not.
>
>  
>
> There is more! P. 2274 there is a general denouncement of morphological
> cladistics! "The problem with using apomorphies for the reconstruction
> of phylogenetic relationships, however, extends beyond the
> classification of fossils". 
>
>  
>
> "Because gene products essentially defined the phenotype, we can expect
> a certain proportion of derived morphological characters to support the
> sister grouping of humans and gorillas, or chimpanzees and gorillas"
> [but for some strange reason, not humans and orangutans!]
>
>  
>
> So here you have it, on the authority of these expert molecular
> systematists, morphological cladistics is dead!!! (As I have said
> before, it baffles the boffin in my to understand why morphologists are
> so willing (desperate) to make themselves slaves to molecular
> authority)>
>
>  
>
> Am I the only one on this list that thinks this molecular stuff is
> nutty?
>
>  
>
> 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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