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Re: Wukongopterus and Darwinopterus

David M. wrote with regard to phylogenetic analysis:

Of course, the solution isn't to exclude data, it's to include even more -- and 
to recheck the _quality_ of the data: How many typos are in there? How many 
correlated characters? Which characters should be ordered or given a 
stepmatrix, and why? And so on and so forth (Jenner 2001; Marjanovic & Laurin 
2008b, 2009; Marjanovic, Germain & Laurin in prep.).
Size does matter (Emmerich 1998), but so does quality (Kitamura 2004).


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.

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. 

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

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

If there's no question: have at it!~

Then there's also the possibility of competing trees when someone else has a 
different take -- which is always an excellent idea! Brings out the best.

David M. wrote:

Adding data can reveal previously hidden character conflict and thus increase 
the number of MPTs.

In my experience, taking another look at MacClade when loss of resolution 
occurs, always exposes the misrepresented characters score. Evolution abhors 
apomorphies, preferring parsimony. Apomorphies do exist. They're just rare and 
like feathers, nearly always shared by "birds of a feather." Also, a good, 
healthy tree of sufficient size can sustain many dozens of typos, if not all 
concentrated near a weak branch.

"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. "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. 

David Peters
St. Louis