Re: New paper on Neoaves

[Tim Williams <twilliams_alpha@hotmail.com>]

Mickey Mortimer wrote:

> Or maybe Amphioxus isn't a chordate.

That's a tough sell.  Notochord, pharyngeal slits, myotomes...?

> There have been a ton of new basal deuterostome discoveries lately, and the 
> molecular analysis of Delsuc et al. (2006) seemed fine with that 
> arrangement.

Well, I had thought Delsuc et al. (2006)'s claim to fame was that they found 
strong support for tunicates being closer than amphioxus to vertebrates.  
They found only weak support for an echinoderm-amphioxus group (it wasn't 
any better supported than a monophyletic Chordata); but no evidence for an 
echinoderm-chordate clade (and hemichordates were omitted).  Some years back 
there was a flurry of interest in an echinoderm-chordate link, by way of the 
fossil homalozoans ('Carpoidea'); but this idea seems to have fallen by the 
wayside.

> Also the phenotypic results of the nucleotide changes are often difficult 
> to determine.

I know you're addressing David's point, but I would take this opportunity to 
mention that I don't think that this is important for molecular-based 
phylogenetic analyses.  What I think is essential is a better understanding 
of the genes and proteins themselves before we become too carried away with 
molecular-based analyses.  So many phylogenetic analyses pin their hopes on 
protein-coding genes (including their introns) without understanding why or 
how the changes at the level of DNA or protein actually occurred.  The 
amount of homoplasy caused by biochemical constraints may be vastly 
underestimated.

Oh dear, I'm veering way OT.  Back to avian theropods.... the thing is, I'm 
deeply suspicious of this Metaves-Coronaves split, and the constituent taxa 
within each.  Some signal is undoubtedly 'real' - particularly the more 
recent divergences.  But I hope the study of Ericson &c (and similar 
studies) doesn't prompt people to start erecting a host of new 
molecule-based clade names, such as happened with mammals.

Cheers

Tim