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Re: bat origins - the smoking gun: guidelines



> 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.

Great! I just meant to say that you won't find any competition, at least not on this list. :-)


> 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.

Why? There are 3 possible trees for 3 taxa. Every trichotomy is an unsolved "three-taxon problem". Sure, the situation that you'll have only 3 taxa _in your entire matrix_ is rather hypothetical.


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.

Sorry, I only took binary characters into account. :-] To get a fully (!) resolved tree, every clade in that tree must have at least one autapomorphy, so there must be at least as many characters as taxa in the matrix _if every character has 2 states_. If there are more states per character, fewer characters can in principle (!) suffice.


> 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.

Then ignore this case and take a few others. I've seen at least one analysis with several megabats and many microbats. (The latter turned out to be paraphyletic.)