Re: Prolacertiformes and Protorosauria

[Mike Habib <habib@jhmi.edu>]

On May 17, 2009, at 9:05 AM, David Peters wrote:

> Yes, there is some intuition that goes into judging results.

When I do phylogenetic reconstruction (or when I review the  
reconstructions that others have published), I try very hard not to  
judge by intuition - if we do that, then we might as well build the  
trees "by eye", exactly as was done pre-cladistics.  Part of what is  
so useful with matrix-based phylogenetic reconstruction is it allows  
you to find well-supported hypotheses that you would have otherwise  
overlooked because they are counter-intuitive.  Intuition has it's  
place, but I'm not sure this is it.

> ie. placing mesosaurs with pareiasaurs = bad.

Ah, but how do we know it is "bad"?  Perhaps we get a quick intuitive  
twinge that tells us something might be amiss, but if you actually  
want to add some weight to such an assertion, you have to demonstrate  
that something isn't right more objectively (I'm not saying that  
mesosaurs and pareiasaurs must be related, incidentally).  For  
example, perhaps the taxa in question almost never come out together  
in any trees that anyone runs, with various character sets, except for  
one dataset with a very limited number of taxa or characters  
included.  Then we might be able to, with some degree of objectivity,  
indicate that the "bad" clade is indeed likely to be a fluke, because  
alternative pairings are supported in other trees that seem to be more  
robust in their methodology.  Or perhaps consistency index or branch  
support metrics suggest that a given topology is weak.  Stratigraphic  
indices might do the same.  There are a lot of data-driven ways to  
demonstrate that a given clade composition is questionable.  It's  
important to knock them down with data, though, rather than our own  
sensibilities, alone.

> More importantly, there is some experience at work here too. Yes,  
> I've done the larger, more inclusive study, that indicates the  
> breaks are real and taxon exclusion is the culprit.

Alright, that might be more informative - the question I have here is  
how does the larger, more inclusive study indicate that the breaks are  
real?  I presume are you saying that you get a different topology with  
your dataset than the one published.  No problems there - the question  
then becomes: why is your tree more robust?  Just because it has more  
taxa doesn't mean it's more accurate.  It *might* be, but other  
indicators are important.  It might be case that we have no objective  
reason to prefer one tree or the other at this time, in which case we  
simply have two alternative topologies, each with some support from  
data.  That's fine, and happens all the time, but to really push one  
topology as "better" requires more than an intuitive sense through  
experience (though intuition and experience don't hurt).

> As for your 'by definition' comment, yes. True. Even so, 'by  
> default' is also at work here. The authors were working from too  
> large a gamut and too small of an inclusion group to make sense.  
> There are better sister taxa out there. The larger study would have  
> revealed this.

I see what you are arguing, but consider this: if we are to judge  
trees entirely by how many taxa they include, does that then mean we  
cannot trust any phylogeny for, say, Amniota that does not include  
every amniote known?  Clearly there are thresholds in there somewhere  
that we recognize - so, stepping back and being a little less extreme:  
what percentage of the group do you need to be confident?  Keep in  
mind that for any large fossil vertebrate lineage, you might be  
working with 1%-10% or so of the taxa that actually existed.

Cheers,

--Mike



Michael Habib, M.S.
PhD. Candidate
Center for Functional Anatomy and Evolution
Johns Hopkins School of Medicine
1830 E. Monument Street
Baltimore, MD 21205
(443) 280-0181
habib@jhmi.edu