ancient DNA

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This is a copy of a reply to Tom Lipka that I thought might be of interest.
>Hi Chip,
>   Your probably buisy with the new semester like all of us are so I am just
>keeping in touch.  Hows your DNA analysis coming along?  Any interesting
>results?
>
>                                  Anxiously waiting for the results ;-)
>
>                                         Tom Lipka
>
>
Reply follows:


Hi Tom

Things are a little hectic, like buying new parking stickers and dealing
with the incoming student traffic. However, I don't know if you heard, but I
got 18S ribosomal sequence from an Ornithomimus, maybe a Struthio(Phil
Currie submitted this specimen), that is 98% homologous with the
Tenontosaurus sequence I recovered in the spring. These two sequences clade
out together smack dab between Reptiles and Mammals, so far. I am only
aligning about 340 bases of clean read.  The fact that the sequences were
generated from different bones months apart with different reagents and
equipment, (the Tenontosaurus material was not in the lab at the time of the
Ornitho work), and that the two are closely related to each other and
nothing else, is very supportive.  I am getting more sequence weekly, I have
nearly 700 bases of the gene from each dino, and I will keep you updated.

As to your material, I am going to get to it, but I still have some stuff
Ostrom sent me before your shipment.  I am doing this in order of receipt of
the specimens.

I also recovered 145 bases of Cytochrome B sequence from the Tenont.
Couldn't get any part of that gene from the Ornitho, it just isn't there. I
don't know how informative this cyto B sequence will be, although a cursory
glance indicates some amino acid replacements that are unique when compared
with mammals, birds and fish.

Curiously, parts of the 18S gene are recovered at a higher frequency than
others, this with only two dino bones of course, so get out the salt shaker.
This may reflect properties of that particular part of the gene that lend to
greater stability (some nucleotides are more unstable than others over
time), or this just might be a coincidence. We'll see.

The Ornitho bone was very unpermineralized. The Tenont bone not so.  I
tested rib bone from the Tenont and got nothing, whereas the productive part
was actually ossified tendon from the tail. It may be that, upon death, the
tendon in the tail, being covered with thin skin, dessicated rapidly, while
the rib cage held decaying guts and was subject to less favorable conditions
for preservation of DNA. Again, pass the salt please.

I am going to send this over the net to see what response it generates. 

-Chip