corroboration

[Jim Whitfield]

In a discussion of John Wenzel's paper, Doug Yanega wrote:

>To quote Wenzel's recent paper, after he gives a list of known (published)
>limitations and problems with the bootstrap, he concludes; "It is also
>important to note that the ordinary application of bootstrapping procedures
>is to derive a confidence interval for the estimate of a parameter of a
>distribution (Manly, 1991), and that statistical mean and variance do not
>apply to unique historical identity of the phylogeny (Wenzel & Carpenter,
>1994). So, although the bootstrap values mean something, it is not clear
>what they mean exactly, and it is clear that they do not mean the same
>thing when compared across different trees. It would seem that these
>objections would suffice to exile the bootstrap from its current place of
>honor." He suggests that Bremer support values are more informative, but
>notes; "...these are not intended to serve as statistical confidence
>tools."

It would be apparent (I think) to most phylogenetic systematists that the
use of the bootstrap literally to derive a confidence interval has declined
considerably in recent years, and that it is used mostly as a relative
indicator of support, complementary to the Bremer support measure.  This is
not because means and variances do not apply to our *estimates* of a
phylogeny.  The *correctness* of the phylogeny cannot be inferred from the
statistical measures, but the degree to which one can make statements from
one's data CAN. In the case of the bootstrap, there are some limitations
and problems, as has been discussed in more detail by Sanderson (1995,
Syst. Biol. 44: 299-320). Strict cladists seem not to want to accept that
the methods associated with parsimony analysis do come with assumptions,
and that they are not simply a direct translation of Occam's Razor to
nested sets of hypotheses of homology (as suggested below).


>I think it would be fair to say that cladists do not view ANY of this
>process as having or requiring statistical properties, and therefore view
>attempts to include probabilistic or statistical approaches in phylogeny
>reconstruction as misguided at best, and misleading at worst, stemming from
>a preoccupation with *process*-based models (e.g. max-like) which are NOT
>compatible with parsimony-based cladistics. Parsimony is not a process
>model - it is Occam's Razor applied to a nested set of hypotheses of
>homology. The kinds of tests you want to apply appear to be inappropriate
>for cladistic analyses.

This is a fair statement concerning *some* cladists, but certainly not a
majority of phylogenetic systematists as a whole community.  I certainly
would not suggest that there is general agreement on a set of statistical
(or other support) measures that is problem-free, but in my view it is
misguided to claim that our work cannot be not subjected to the same
standards of data analysis as other aspects of science.
                                                Jim Whitfield

James B. Whitfield
Associate Professor
Department of Entomology
321 Agriculture
University of Arkansas
Fayetteville, AR 72701
phone (501)575-2482
FAX (501)575-2452
jwhitfie at comp.uark.edu