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

["Thomas R. Holtz, Jr." <tholtz@geol.umd.edu>]

> From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu]On Behalf Of
> david peters
>
> What I'm suggesting is this:
>
> Start with 100 taxa. A heuristic search breaks them into two groups of  45 
> and 45 plus 10 outgroup taxa.
>
> Knowing that the most derived taxa will have little affect on the most basal 
> taxa (after all, they've already contributed
> their DNA long before), is there any problem when I delete the most derived 
> 30 taxa from each clade leaving the 10
> outgroup taxa plus 15 basals from each taxa? That makes 40 rather than 100. 
> Later analyses can each take up the rest.
>
> I mean, dino people are doing essentially the same thing by not including 
> parrots and hummingbirds in Cretaceous
> dino-bird analyses.

Okay, this is a good plan. So long as you include a smattering of the forms 
from the sister group, then you should bet more useful
results.


> From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu]On Behalf Of
> Jaime A. Headden
>
>   Sereno has done this for his large analysis in 1999, and Carpenter did this
> in 2001 for Ankylosauria.

However, they were correctly criticized for this because their particular 
analyses would have been incapable of testing some of the
important conclusions they were hoping to test. For example, not running 
Alvarezsauridae and a bunch of different bird taxa in the
same analysis means you can't test the hypothesis that alvarezsaurids are basal 
birds; and running polacanthids, nodosaurids, and
ankylosaurids in separate analyses means you can't test the hypothesis that 
polcanthids are paraphyletic with respect to
Nodosauridae (traditional sense), Ankylosauridae (traditional sense) or both.

                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

http://www.geol.umd.edu/~tholtz/
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