RE: New paper on Neoaves

[Tim Williams <twilliams_alpha@hotmail.com>]

Mickey Mortimer wrote:

> I wonder.... how many well supported (>95% Bayesian or bootstrap) molecular 
> nodes have later been 'disproven'?  And of the ones that have been, in how 
> many cases was it a matter of needing to throw more taxa or bases in the 
> analysis?

You and David hold to the assumption that homoplasy is random, and can be 
overcome simply by enlarging the dataset or expanding the taxon sample.  
Thus, the phylogenetic signal, which denotes a common and shared ancestry, 
should eventually overcome this randomly distributed 'noise'.  But with 
genes and proteins, this is often a brave assumption to make.

Here's one case that highlights the problem.  Naylor and Brown (1998) used 
over 12,000 bases (from 19 mitochondrial genes) and recovered 100% bootstrap 
support for a clade that comprised vertebrates and echinoderms to the 
exclusion of amphioxus (lancelet).  This topology was recovered regardless 
of the method of analysis.  The authors didn't believe their own tree, since 
it is contradicted by compelling morphological evidence that vertebrates are 
closer to lancelets than to echinoderms.  They argued *against* simply 
accruing even more taxa or even longer datasets (not possible for the 
mitochondrial genome - they had already used every gene!).  Instead, they 
favored investigating the underlying factor(s) that are pulling the 
vertebrate and echinoderm sequences together, and dispute the assumption 
that homoplasy ('noise') is distributed randomly in the dataset.

I know I'm on my hobby horse here, and I apologize for the verbose postings. 
 But the thing that is obvious about *morphology*-based phylogenetic 
analyses is that they are almost always followed by a discussion of which 
morphological characters (synapomorphies) unite which taxa.  In other words, 
it's plain to see the identity of the characters that diagnose certain 
clades.  This rarely happens with *molecular* clades.  Here, the characters 
are at the level of genes and amino acids, and the structural and functional 
properties of the sequences are skimmed over.  Instead, researchers tend to 
focus on bootstrap support (or posterior probabilities, in the Bayesian 
world) as the final determinant for a 'good' tree, and move on.  However, 
I'd like to see more discussion of the gene- or amino-acid-level factors 
that are responsible for the topology of the tree.  For example, what 
sequence-level characters are putting Coronaves together, or pulling 
Falconiformes apart?

Cheers

Tim