Re: New paper on Neoaves

[David Marjanovic <david.marjanovic@gmx.at>]

> > Sequencing (from organism to GenBank submission) is a matter of a week or 
> > two, you download the other sequences from GenBank, and then you let the 
> > computer run for a couple of weeks. That's all.
>
> Hey, come work in my lab!  You do it a lot faster than I do.  :-)

Maybe I should add that in the three-week course I'm talking about we 
immediately got serious amounts of DNA out of the bivalves and scaphopods, 
and the genes for cytochrome c oxidase and 18S rRNA are not so big that the 
computers would have needed weeks. We were told that to get DNA out of 
woodlice you have to put them into an exsiccator alive because every other 
imaginable method lets the DNA be destroyed by whatever enzymes there are 
swimming around in a woodlouse. :-S

> In some cases, they still are.  I don't think molecular phylogenies have
> 'solved' the problem of placental phylogeny, in spite of those
> well-supported sequence-based clades.

Except for the precise topology of Afrotheria and the exact position of the 
bats within Laurasiatheria, I think we can be pretty sure about the standard 
molecular placental phylogeny, even if only because it always comes out, no 
matter which genes are used, and no matter how many taxa are added. It's 
just frustrating that there is no morphological analysis of similar size 
that we could compare.

> We tend to use molecular-based
> analyses to make up for the deficiencies of morphology-based analyses
> (incomplete fossil record, convergence, etc).  But I tend to believe that
> these deficiencies carry over into molecular phylogenies too, though 
> they're
> expressed in different ways.

Long-branch attraction of turtles in both molecular and morphological 
data...

> There are very few mammal "orders" for which we can document their early
> evolution (whales are an exception; but they weren't part of this 
> radiation).

Rodentia and Lagomorpha, no, Simplicidentata and Duplicidentata have a great 
fossil record in the Paleocene of China and Mongolia, but no others are 
comparable.

> But if placentals
> did undergo a phase rapid evolution, with the divergence of many lineages 
> in
> a relatively short period of time, we may be asking too much of molecules 
> to
> capture the exact order in which these lineages diverged.

This is of course where fossils are supposed to come in handy.

> > Does NOBODY care how xenungulates fit in?
>
> I do!  Poor _Carodnia_....  :-(

Quite so.