James Francis Lyons-Weiler weiler at ERS.UNR.EDU
Wed Mar 5 07:17:37 CST 1997

Tom D commented:

>In fact, parsimony will result in resolved trees given random data, a
that is >apparently surprising to some practicioner.

>Well lets be precise here. A parsimony criterion may reveal a
>best-supported pattern in data which was generated under
>conditions which were designed to be random. If there is a
>pattern which emerges from the sea of randomness, then what
>is one to say? What are you saying? Does the parsimony
>algorithm reveal a truly spurious best-supported
>pattern when no such thing really exists (how would it do that?) or
>is it that small "random" datsets or datasets resulting from "faulty'
>randomness generators actually have best-supported patterns within

The answer to the first question (does the parsimony algorithm reveal a
truly spurious pattern) is, precisely, yes.

How would it do that?  There exists for EVERY matrix (with variable
states among taxa) a set of shortest trees.  This is true whether
the data are random or not, and it is true for large (1,000 of taxa,
1,000s of characters), or small, and it is true whether one uses a random
number generator or pulls marbles from a bag.

Try it!



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