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Re: Rconstructing DNA (was Re: Dino-fuzz found in amber?)

> Are you sure it doesn't involve phylogenetic bracketing right from
> the start, so that you need a bird _and_ a crocodile -- or, rather,
> the ancestral neornithean and the ancestral (crown-)crocodylian
> sequence -- _before_ you start comparing the *Tyrannosaurus* aa
> sequence to anything?

 "If we had the crocodile or alligator or caiman sequence the
 comparison could be improved."

 "It would make difference, since it could help in philogenetic
 bracketing." http://dml.cmnh.org/2011Sep/msg00210.html

 "And, naturally, outgroups."

Read what you quoted from me again.

> Absolutely not. All conclusions about them are drawn from
> _inter_polation: you compare descendants and draw conclusions about
> their common ancestor. You do not go beyond that.

 Sure. But no one is going *beyond*.

You are. You have neornithean sequences (or even just one), yet you don't merely reconstruct the ancestral neornithean sequence -- you reconstruct the ancestral tyrannoraptoran sequence! That's extrapolation.

 We do similar things when we find a incomplete fossil. We know that
 the ancestral dinosaur is a tetrapod with all four limbs (and it is
 known by comparative analysis of the descendants). We find a
 dinosaur skeleton with three limbs: we could infer that the
 individual used to have four limbs (unless we find information that
 lead us to conclude other way).

First, this is, again, interpolation. Second, information reconstructed this way is _never_ used in phylogenetic analysis -- is that what you mean?