Re: Prolacertiformes and Protorosauria

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

----- Original Message -----
From: "Mike Habib" <habib@jhmi.edu>
Sent: Tuesday, May 19, 2009 10:02 PM

> The number of MPTs is not actually a particularly strong measure of
> the robustness of the tree.

One reason is that it often happens that a taxon can occupy two equally 
parsimonious places in the tree, _no matter how robust the rest of the tree 
is_. (Especially when it's incompletely known and/or there are just too few 
characters in the matrix.)

> Surviving decay tests is a better
> indicator, but it still doesn't actually tell you if your dataset is
> stronger than another dataset - it indicates whether or not you are
> confident reporting the MPT in question, relative to the next-most
> parsimonious trees.  Decay tests are mostly a way of approaching the
> issue that biological systems are not actually parsimonious.  If you
> can relax the parsimony requirement a great deal, and still recover
> the same topology, then the tree is at least robust to that particular
> assumption.

Good explanation.

> However, those indices do not answer the question of preference of 
> topology *between* datasets - when two different matrices produce 
> different topologies, then decay indices alone are not particular 
> informative.

The right thing to do here is the most work-intensive one possible: Either 
fuse the matrices and see what this total-evidence approach produces. Or 
look for errors in each matrix and see what happens if you correct them. Or 
of course both.

The second is what I'm doing with tetrapod phylogeny. The first, and to a 
small extent the third, is what I'm doing with amniote phylogeny. And 
together that's a PhD thesis.