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RE: Bootstrap question; & a v? for Dan Varner

> From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu]On Behalf Of
> david peters
> The problem I've been having is replicate hangup, where a single replicate 
> takes several hours with 99 to go. Very
> discouraging. Is there any sin to divide and conquer? i.e. splitting up the 
> big cladogram into smaller parts for
> analysis? That appeared to give the right answer.

In two words: EEK and EEEK!!!

A) One doesn't know if an analysis gives the "right answer." That's the reason 
for doing analyses: we don't know what the real
branching order was like, and so we use analytical techniques to approximate 

B) Breaking a big cladogram up into smaller parts carries with it a major 
problem: namely, you automatically restrict the possible
sets of trees, and not necessarily in a useful way. For example, if you were 
interested in testing the position of alvarezsaurids,
and most specifically the hypothesis that alvarezsaurids were nested WITHIN 
birds closer to modern birds than is Archaeopteryx, than
to do this fairly you would have to run an analysis that included both 
ornithomimosaurs and various groups of birds (and not just a
single Avialae OTU).

Or alternatively, if you hypothesized that Caudipteryx might be be a bird at 
all, but was in fact basal to the whole
dromaeosaurid-bird clade, than you shouldn't break up the analysis such that 
you only include Caudipteryx in the part that doesn't
include any taxa outside the bird-dromaeosaurid clade!!

That both the above have been done by smart, well-resepected paleontologists 
doesn't mean that they were good analyses. In fact, it
was only when they (and others) did larger, more comprehensive analyses that we 
started to get results that are better defensible.

Yes, long run times are boring. And occupy your computer. But that is part of 
doing science. Just want to point out that REALLY big
analyses (like the major angiosperm ones, and some other 100s of OTU analyses 
out there) take months of processing time. Them's the
breaks, unfortunately.

                Thomas R. Holtz, Jr.
                Vertebrate Paleontologist
Department of Geology           Director, Earth, Life & Time Program
University of Maryland          College Park Scholars
        Mailing Address:
                Building 237, Room 1117
                College Park, MD  20742

Phone:  301-405-4084    Email:  tholtz@geol.umd.edu
Fax (Geol):  301-314-9661       Fax (CPS-ELT): 301-405-0796