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Re: Prolacertiformes and Protorosauria
On May 19, 2009, at 7:27 PM, David Peters wrote:
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
I'm not sure if you mean 14x by taxon number, character number, or the
product of the two (i.e. total matrix size), but in any case, having a
much larger matrix has its advantages. However, it is worth noting
that increased taxon sampling does not necessarily provide a better
answer - Scotland et al. (2003) discussed this property, and
simulation tests have demonstrated this somewhat counter-intuitive
result. That's not to say that you don't have an interesting result:
you have shown an important taxon sampling effect. The question that
remains is: what exactly about the inclusion sets is driving the
topology changes? Can get some measure of confidence between the two?
The larger set is more practically useful *if* the topology is stronger.
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
That saturation effect is not altogether unexpected, and it is
interesting - I'm not sure what it really says about topology
confidence, though. I'd have to see some simulation results to have a
better feel for the empirical ramifications. I do like the
sensitivity analysis approach, though, for what that's worth. I'd be
quite curious to hear what the theoretical phylogenetics crowd has to
say about these effects.
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.
If that is the reason for exclusion, I agree. But if an author
excludes a taxon because they don't feel confident in coding it - it
is fragmentary, or they have not had sufficient access to the
specimen, for example - then it might be justified.
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.
They don't have to remain with the same sister taxon - it is quite
plausible (and reasonably common) for a taxon to move substantially
throughout the tree, without any change in total calculated parsimony
(i.e. total tree length is constant).
Michael Habib, M.S.
Center for Functional Anatomy and Evolution
Johns Hopkins School of Medicine
1830 E. Monument Street
Baltimore, MD 21205