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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