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Re: Wukongopterus and Darwinopterus

On Nov 27, 2009, at 8:23 AM, David Peters wrote:

When the tree topology is correct typo corrections will support the tree. When not, typos will correct a tree. The correct tree is/was out there. It just has to be echoed in analysis.

Hypothetically. Realistically, though, we will never have the "right tree" for any given group - every topology will be inaccurate in some detail (if nothing else, we don't have all the species that ever existed). Therefore, in all likelihood, every topology is "good" in some places and "poor" in others, and how typo corrections will affect the various parts of the topology is much more complicated than it might seem (if nothing else, how do you know what got "better"?) If you're getting the "right" tree with typos, then you're getting the right thing for the wrong reasons, and there's actually no way to tell that you were close in the first place. In the end, the only thing to do is correct errors as they are identified: typo-free is always better, regardless of what happens to the tree.

Correlated characters? How difficult to determine: 1) long neck vs. long tail on sauropods; 2) short manual toes vs. short pedal toes on stegosaurs; 3) wide skull vs. orbits on skull roof on batrachomorphs; 4) number of caudal vertebrae versus loss of teeth in birds, etc. etc. etc. The list is endless.

Yes, the problem is difficult. However, presuming that traits are not correlated because we do not wish to deal with the complexity is not the right solution.

ordered vs. unordered: so difficult to determine with convergence and parallelism. Just look at any misnested taxon.

How do you know they're misnested?

Best to just let the suite have its say-so if there's any question.

Presuming you mean everything should be unordered and ignored for correlations, there are quite a few manuscripts in the cladistics literature that suggest otherwise.

In my experience, taking another look at MacClade when loss of resolution occurs, always exposes the misrepresented characters score.

If you find misrepresented characters, then that's a good catch. However, low resolution does not mean a tree is "bad". Sometimes, low resolution is the correct answer given the data at hand: it simply means that taxa cannot be differentiated in a repeatable manner according to the present data. That may be the error-free, robust answer for a given dataset.

Evolution abhors apomorphies, preferring parsimony.

Really?  News to me.

Apomorphies do exist. They're just rare and like feathers, nearly always shared by "birds of a feather."

Rare? News to me again. And yes, obviously the shared ones (i.e. synapomorphies) are particularly interesting, but I'm not sure where you're going with this.

Also, a good, healthy tree of sufficient size can sustain many dozens of typos, if not all concentrated near a weak branch.

Is this based on a particular simulation study? Obviously, if a tree is very large, and contains six or seven typos, then the errors are a smaller percentage of the dataset than in a case where the same six or seven typos exist in a small dataset. However, I'm not sure what this means for "sustaining" typos, or how a matrix with many errors would still be considered healthy.

"Weasel" words (i.e. could, can, might, may, would, should, possibly, recheck the quality, correlated, heterodox, believe, etc. ) are signs that specific data are being side-stepped.

Actually, they're signs of uncertainty, which is a pretty basic aspect of science, and therefore a common issue. Yes, sometimes such terminology indicates a cop out. Often, it is just being realistic. (Are bats closely related to primates? Well, the *might* be, as some trees support that - but most trees these days don't, so it's *likely* they do not - this is just a realistic assessment of the situation).

"An apple a day keeps the doctor away" is a falsifiable statement. An apple a day (can, may, is believed to) keep the doctor away" is not. I trust no referee who relies on weasel words when falsifiable data is on the table.

Which falsifiable data are in question in the present case?

--Mike H.

Michael Habib
Assistant Professor of Biology
Chatham University
Woodland Road, Pittsburgh PA  15232
Buhl Hall, Room 226A
(443) 280-0181