RE: Bootstrap question;

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

David Peters (davidrpeters@earthlink.net) wrote:

<I mean, dino people are doing essentially the same thing by not including
parrots and hummingbirds in Cretaceous dino-bird analyses.>

  Unfortunately, this is not the same thing as excluding, say, *Utatsusaurus*
from an analysis of the phylogeny of Ichthyopterygia. This is more akin to
lumping all birds into one group (say, Neornithes) that is agreed upon to be
consistently monophyletic (yes, an a priori assumption) by many, many more
analyses than have sampled dinosaurs not including birds. So, this is like
doing an analysis of Canidae and using only *Canis lupus* in the matrix and
excluding other *Canis* species. Some taxa may be so remarkably identical that
it would be pointless to include their data in the matrix since apart from two
or three positions, the codings are the same. When calibrating whole-mammal
mtDNA trees, we tend to use human and mouse mitochondria alone to sample
eutherians. This is not a flaw, but part of the hypothesis. Other analyses
point to other possible included taxa as closer to some particular otu's
without variation or with only minor unexceptional variation (such as Forster's
position of troodontids versus birds and other maniraptorans).

  Cheers,

Jaime A. Headden

  Little steps are often the hardest to take.  We are too used to making leaps 
in the face of adversity, that a simple skip is so hard to do.  We should all 
learn to walk soft, walk small, see the world around us rather than zoom by it.

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


                
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