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Re: bat origins - the smoking gun: guidelines




DMarjanovic wrote:
Well -- those guidelines are guidelines for conducting a phylogenetic
analysis. Nothing wrong with them. Except that I don't think anyone of
us has the time to compile a phylogenetic analysis of Placentalia right
now. So I don't quite understand what your point is.

>>>>> I'm about to embark on the study. I have the time between now and
whenever. I'm just offering the same opportunity in friendly
competition.


         I say 'taxon selection is everything', but that is really true
only
         after a certain minimum number of characters are employed from
every
         corner of the body,  I found that 150 will get you 95% there
and 225
         will provide well.


Depends on the number of taxa. To choose really trivial examples, you
most probably won't need 150 characters to resolve a tree with three
taxa,
while 150 characters are incapable of resolving a tree with 1000 taxa.

>>>> If you're only trying to resolve 3 taxa, then you've a priori
decided on/understood the situation and the analysis is essentially
moot. I don't have experience with 1000 taxa, but I can tell you that
with 250 taxa, many represented by only skulls or only post-crania, 150
characters will get you 95% of the way there, and 225 characters will
take you to a single tree, as I mentioned earlier. Will you please tell
the list about the 1000 taxa analysis and where it can be found to be
tested? Or is that a hypothetical list of taxa and characters?

         3. Avoid suprageneric taxa like the plague.


Molecular data matrices are almost always completely devoid of them.
OTUs in molecular matrices are by default specimens.

         The study of the ancestry of bats has suffered from all of the
above.


I disagree. The latest molecular studies (of the last few years) have
very broad and ever-increasing taxon samples, large and ever-increasing
numbers of characters (the latest JVP contains one with 22 genes!), and
have specimens as OTUs.

>>>>>> Yes, molecular matrices are specimen based, but ironically, and
others have published cautionary papers on this, the wrong
representative has been elected in this case to represent the clade with
its blood work.

David Peters
St. Louis