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Re: Proteins found in mosasaur bone

--- David Marjanovic <david.marjanovic@gmx.at> schrieb am Sa, 30.4.2011:

> Von: David Marjanovic <david.marjanovic@gmx.at>
> Betreff: Re: Proteins found in mosasaur bone
> An: "DML" <dinosaur@usc.edu>
> Datum: Samstag, 30. April, 2011 10:35 Uhr
> >  I'd like to see what
> sequencing this does to squamate phylogeny.
> Who doesn't :-)
> I just fear not much collagen has ever been sequenced
> (either the proteins or the genes for them).

Well actually a lot has been sequenced (both nucleotide and aa) but the bulk is 
mammalian. Teleosts are also quite abundantly represented but about as useless 
here as mammalian sequences. 

ColI alpha1/alpha2 are fairly sampled for birds (Galloanseres and Zebrafinch), 
which is probably barely sufficient (at least alpha1 is available for several 
Galliformes, which should in fact be sufficient - for such deep divergences it 
is useful to have a 3-taxon outgroup of known internal relationships, as a 
control against LBA mis-rooting[*]. Galloanseres and Passeriformes are not 
ideal - a tinamou, _Anas_ and _Gallus_ would be better - but it's still better 
than a 1- or 2-taxon outgroup which cannot yield reliable results in such a 

But no squamate (or in fact "reptile") ColI sequences I can find on the quick 
except _Anolis carolinensis_. And that is not enough.

But given that antibodies might not be all too specific, sequencing might at 
least clarify if it is in fact ColI they found, and whether it's alpha1 or 



* "Textbook" LBA is readily recognized because it creates low-support 
relationships which look implausible at first glance. It typically occurs where 
the SNR is <<1.

Ingroup rooting LBA is quite typical for regions in the tree where the SNR is 
~1. It is very insidious because it looks as if it *could* be right and 
bootstrap support is often >>80%.

>From the looks of it, the "tinamous are secondarily flightless" idea is based 
>on this kind of LBA. Unrooted, the paleognath phylogeny in Hackett et al. 
>leaves little to be desired.