Re: Reverse-engineering the T. rex genome

[Erik Boehm <erikboehm07@yahoo.com>]

> In other words, the inferred mt sequence for example would
> essentially consist of a few ultraconserved positions and A
> LOT of noise. Noise you couldn't even try to resolve,
> because the branch you're trying figure out has no crown
> taxa at all.
> 
> 
> Eike

I wasn't proposing this as a way to reverse engineer a T-rex genome, but rather 
I think this would be the closest I think one could get to "reverse 
engineering" something that was extinct.
Looking at consensus sequences will give you a much better approximation, then 
identifying what genes are involved with infection by a pathogen, and 
extrapolating from those genes, a *guess* at what the genome of an extinct 
species that suffered from a similar pathogen *might* be like.

An engineered organism using a consensus sequence with strong statistical 
backing will not be the same as the ancestral organism, but I do wonder if it 
would be viable, and how close we could come to the ancestral animal.
I already acknowledged the possibility it may be a "monster of science" (if it 
is even viable), with no relevance to the ancestral organism.




To have even a reasonable chance at getting a good approximation of an 
ancestral genome, you would need a lot of crown species, from pretty evenly 
distributed branching.

You certainly couldn't make a good estimate of the ancestral genome sequence of 
Sarcopterygians by sampling one species of coelacanth and a human....
Nor do I think the non tetrapod Sarcopterygians are well represented enough to 
arrive at a good approximation of an ancestral Sarcopterygian genome, (2 
coelacanth species and 4 lunchfish species?).


I wonder how well one could align the genomes of domesticated dogs, and how 
statistically "strong" the resulting consensus sequence would be.
As a side note, did dogs arise from a single "domestication event"? or were 
they domesticated independently in different areas from local canine 
populations (given that various wolf and coyote species are known to produce 
viable hybrids, dogs could be hybrids from separate domestication events)?

If you had an ancestral sequence of ATCG, and you have only 2 crown species 
with a sequence AGCG and ATAG, you have no hope of determining the ancestral 
sequence (beyond saying it was likely A**G).

Moreover, at the nucleotide level, there may be no way of distinguishing 
independently evolved nucleotide sequences.
While Raisuchians and dinos independently evolved erect limbs, its possible to 
tell the difference between them.

If one goes from ATCG -> ATCC -> ATAC, and the other one goes ATCG-> ATCA -> 
ATAA, you may assume the ancestral sequence was ATA* when in fact it wasn't.
This is particularly relevant to highly variable regions where the sequence 
doesn't seem to matter at all (its as if sometimes the nucleotides are there 
just to maintain spacing between other conserved elements, but there are other 
explanations for highly variable regions), where at a first approximation, a 
point nucleotide mutation has a 25% chance of being identical to an independent 
mutation at the same position.