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Re: Prolacertiformes and Protorosauria
Mike,
The data set in question is 14x larger than any prior published data
set covering the same taxonomic spectrum. With it I can reduce the
dataset to the size of the smaller ones and often (not always) get
their topology. Adding taxa to see if the tree shifts has also been a
good test of tree topology. At some point in the addition process,
tree shifts become less and less possible because you're reaching a
saturation point where the weight of the rest of the tree is becoming
harder to shake.
If the lack of confidence and lack of resolution are the result of
taxon exclusion, then PAUP offers a clue that some or all of those
excluded taxa are better off included. All I've ever asked for is
inclusion. If someone excludes pertinent and previously taxa to
protect a precious hypothesis, then they're doing a disservice to
their own studies. Key now is to figure out how the amniote tree in
toto is built. THEN we can examine each resulting branch with greater
confidence. Make sense?
David Peters
and to David M's reply to Mike's reply:
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.)
>>>>>> Should be right next to the same sister taxa, though. They're
never widely separated (given the above parameters). Important
distinction left unsaid. And this is due to the fact that some
sisters are really different, or not much is known of one or the
other or 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.
>>>> Do it and do it well. We are with you.
David Peters
On May 19, 2009, at 3:02 PM, Mike Habib wrote:
David Peters wrote:
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 number of MPTs is not actually a particularly strong measure of
the robustness of the tree. 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.
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. If one of the matrices produces many MPTs, with
sensitivity to decay tests, then that particular analysis is
hypothesizing a lack of resolution - such a result essentially
indicates that we don't have a good idea of the answer. If the
competing matrix finds few MPTs, containing clades robust to decay
tests, then we have the opposite result: that analysis would
support the conclusion that we have high confidence in the
relationships. The problem is that, without additional
information, we have no way of judging which hypothesis is correct:
a lack of knowledge result is no less plausible than a presence of
knowledge result.
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
David Peters
davidpeters@att.net