RE: New paper on Neoaves

[Michael Mortimer <mickey_mortimer111@msn.com>]

Tim Williams wrote-

> I'd hate to think that there is a belief that you can 'improve' the 
> phylogenetic signal simply by expanding the dataset (=stringing together 
> more and more DNA sequences).

Er, can't we?  Isn't this the whole idea behind supermatrices (not 
supertrees)?

> Also, are each of the single-gene trees consistent?  Individual gene 
> regions may be better at capturing divergence at a certain level, which 
> means that you're going to get a very muddled phylogenetic signal if you 
> simply string these genes together.

I'd think you'd get a better phylogenetic signal if you did this.  The 
levels where divergence was poorly captured by a gene would be poorly 
supported, and easily overwealmed by another gene that captured divergence 
better at those levels.

> I'm not ready to give up on a monophyletic Falconiformes quite yet.  I'm 
> also a little suspicious of the fact that the analysis failed to recover a 
> monophyletic Palaeognathae, based on _Apteryx_ and _Rhea_.  Perhaps greater 
> sampling of the palaeognaths could have solved this; but this begs the 
> question, how many other clades were not recovered because of inadequate 
> taxon sampling?

Many.  Up to N-1 clades in each polytomy of N (I think).  Ratites were not 
supported as para- or polyphyletic, so their monophyly was not rejected.  On 
the other hand, falconids were clearly supported as not most closely related 
to cathartids and Accipitres.

> As a general principle, does increased taxon sampling even help?  I'm not 
> certain it does.  If a gene is unable to capture the phylogenetic signal, 
> or the analysis is unable to tease out this signal, no amount of taxa will 
> improve the situation.

Yes, increased taxon sampling does generally help.  For instance, an 
analysis can have ambiguity due to character conflicts, but new taxa can 
show which of these characters were convergently developed.  As an example, 
if you had troodontids in a polytomy with dromaeosaurids (sickle claw) or 
ornithomimids (parasphenoid bulla), adding Sinovenator would resolve the 
tree.  If the gene's inadequate for that phylogenetic level, then no, it 
won't.  You'll just get poorly supported trees no matter what you add.  But 
the genes used here were clearly adequate for these levels, as we have so 
many branches supported by >95% posterior probabilities.

I suppose I don't get what you're worrying about.  If we have extremely well 
(>95%) supported nodes, then we know things are working.

Mickey Mortimer