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Re: Prolacertiformes and Protorosauria
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
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
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.
Michael Habib, M.S.
Center for Functional Anatomy and Evolution
Johns Hopkins School of Medicine
1830 E. Monument Street
Baltimore, MD 21205