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Re: Dino DNA



A few clarifications regarding molecular systematics:

1) The assumption that the *T. rex* sequence is an artifact is silly.  Any
bacteriologist knows that maintaining aseptic conditions in a test tube (or
an eppendorf tube) is easy.  The chance of contamination and the actual
frequency of its occurrence is nearly zero.

2) If contamination should occur, it is easy to identify.  If contaminated,
the sequence in question will not be new to your data base.  It will align
with, and be identical to, a sequence that is already in your computer.

3) Regarding similarity of the *T. rex* sequence to a bird (or any other
chosen outgroup):  There is very little information regarding the mean
sequence divergence between species, as was asked in this forum.  That is
because sequencing is labor intensive and expensive.  Therefore, very few
species have been completely sequenced.  Molecular systematists simply
choose the "appropriate" gene (or hunk of a gene) for the question they are
asking.  This choice is based on trial and error and familiarity with the
literature.  All genes accumulate mutations at different rates.  Genes that
code for histone proteins are identical in bacteria and humans! 
Presumably, this is due to the importance of their products, the
DNA-wrapping histone proteins (i.e., "important" genes do not tolerate
mutations and evolve slowly).  Other areas of the genome, such as the
hypervariable d-loop, do not code for anything.  Therefore, all point
mutations (a change in a nucleotide) are tolerated and retained (because
there is no gene product to worry about).  Blue marlin individuals have
d-loop "fingerprints" because the rate of mutation accumulation is so
rapid.

Therefore, if you wish to resolve primate twigs, you sequence a "rapid"
gene so that there is some difference in the species considered.  A slow
gene (such as 18s RNA) would be identical in all mammals because of their
recent ancestry.  Alternatively, if you were asking questions about the
interrelationships of the entire animal kingdom, you would sequence a very
slow gene (as faster genes would be 100% different by now and all history
would be erased).

So, my bet is that the *T. rex* workers have chosen a gene that is about
15-25% different among most reptiles and most birds.  I am also anxious to
read their results.

I hope this has been helpful.


*******************************
John F. Morrissey
Assistant Professor
Department of Biology
114 Hofstra University
Hempstead, NY 11550-1090
516-463-5517
FAX: 516-565-0098
E-mail: biojfm@vaxc.hofstra.edu
*******************************