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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?
Assistant Professor of Biology
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