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Re: Prolacertiformes and Protorosauria

All good questions, Mike. 
re: Intuition: You don't have to include every type of Iguanodon in a basal 
dino query. That's what I'm talking about. aka Common sense. In the end, taxon 
selection is subjective. It always has been. Always will be. Paleontologists 
will always play to their favorites. Some will even ignore data and play 
unfairly to keep their precious topologies alive.

re: the value of the larger study: If you SAMPLE from the entire gamut of a 
well-recognized and universally accepted clade, like Amniota, or the Mammalia, 
then you have a framework for working with smaller included clades WITHOUT fear 
of someone saying you missed an important taxon that will throw your tree off 
in another direction. Because it's already in there! And here's where PAUP 
really shines because now we can test relationships ad nauseum to see how many 
more MPTs the various moves make. Add a new fossil (like Pakicetus)and watch 
things change though...and that's okay. Paleontology is like a web page. It can 
be refreshed constantly! And should be.

re: 'bad' relationships. Those with very few so-called "synapomorphies." 
Bennett 1996 mentioned that pterosaurs have very few lepidosaur characters and 
Unwin 2006 wrote the same, and that was the paradigm at the time. Now we find 
they had lizard-like eggs. Lizard-like sterna. Lizard-like toes. Lizard-like 
tails. etc. Paradigms and intuition change. That's what keeps it all so 

re: the more robust tree question: The tree that has the fewest mpts and 
survives the most decay tests is the more robust tree. Is it not? In other 
words, the tree in which sister taxa share the most synapomorphies is the more 
robust tree, yes?  The beauty of having a large and wide spectrum matrix of the 
Amniota is, I can reduce the taxon list to just those in the other studies and 
arrive at pretty much the same topology. Then, if the addition of taxa (very 
easy to do with the data in hand) changes the topology, you've got a problem 
alaong with a solution. I can also add taxa as they are discovered and see what 
happens. So far, not much. Statistically it becomes more and more difficult to 
change the topology with every new taxon because the input data is relatively 
small with so many taxa and characters already building the tree. 

re: thresholds: yes, of course, I agree. Remember, there has been no published 
study yet sampling the spectrum of the amniota with say 100-150 generic taxa. 
So, all smaller studies take their chances that their inclusion set is similar 
to the spectral gamut they seek to test. Confidence would rise if the whole 
spectrum could be published first. It would also answer many mysteries.

David Peters

--- On Sun, 5/17/09, Mike Habib <habib@jhmi.edu> wrote:

> From: Mike Habib <habib@jhmi.edu>
> Subject: Re: Prolacertiformes and Protorosauria
> To: davidpeters@att.net
> Cc: "dinosaur mailing list" <dinosaur@usc.edu>
> Date: Sunday, May 17, 2009, 1:34 PM
> 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