Re: Genealogy of Scaly Reptiles Rewritten by New Research

["Jaime A. Headden" <qilongia@yahoo.com>]

Jason (pristichampsus@yahoo.com) wrote:

<And so another molecular tree comes out ass backwards from every morphological
tree.>

  And this is the fault of the gene tree why? 

<Honestly, I think that there is something seriously wrong with either  the
methodology, or the interpretation of these studies.>

  The morphological trees should be considered in greater doubt and worry than
gene trees, not because the gene inclusions tend to give different results, but
because of the doubly subjective nature of morphological trees (not just gene
sequence and taxa inclusion, but taxa, character number, character selection,
and the strongly subjective nature of coding states and assigning states).

  However, I agree that gene trees should find substantial and historic support
across studies before nomenclature is established This has led to, as Mickey
indicated, the problem of Eulipotyphla, Euarchonta, etc.

<Has there ever  been a molecular study on dogs (_Canis familiaris_) or cats
(_Felis domesticus/cattus_)? You know, a study that has the molecular data 
verifying the known relationships between different breeds.>

  Well, aside from the obviously paraphyletic nature of domestic dogs (*Canis
lupus* rather) and of cats (*Felis sylvestris*? otherwise, *F. domesticus*),
bred from various groups of similar but wild populations of North Africa and
Eurasian felines, we do not have any published studies trying to form a
phylogenetic tree of breeds.

  And frankly, I think such a venture would be a game of futility, given the
highly reticulated nature of dog and cat breeds (many breeds bred by crossing
other breeds, backcrossing, selecting for rather bizarre mutants (i.e.,
american bulldogs, pugs, etc.). Not that we will know unless we try. I would
argue we would find a highly reticulate set that would collapse at resolution
unless narrowing the search parameters to specific genes of low frequency of
selection, such as those which aren't sensory, developmental, etc. I predict
that morphological tests would find that breeds show so much similarity, based
on paraphyletic origination and interbreeding, that distinct trees of patterns
of derivation would be impossible, and any patterns incoherent and strongly
dependant on the included data, perhaps triply subjective because of the
reticulation subjective.

  I think perhaps only mtDNA will give us any idea of a picture, but it suffers
from the same problems as other genes, and people will need to sequence several
hundred breeds to provide the desired picture.

<All I see coming from the Hedges et al study, is a lot of backlash and
controversy.>

  Why backlash? It is just a proposed topology. And like mammal studies, I am
sure Blair Hedges will simply regard the names relative to the given topology,
and plenty enough mammalogists seem to have no problem discarding one topology
for another and picking and choosing names. Careless, but they have a
philosophy after all.

  Cheers,

Jaime A. Headden

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)


        
                
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