Re: Wukongopterus and Darwinopterus

[Mike Habib <habib@jhmi.edu>]

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
mhabib@chatham.edu
(443) 280-0181