compatibility criteria vs. parsimony

Joe Felsenstein joe at evolution.genetics.washington.edu
Thu Oct 5 07:14:27 EST 1995

In article <44u1bu$jds at netnews.upenn.edu>,
Tandy Warnow <tandy at central.cis.upenn.edu> wrote:
>this is a request for a discussion of whether
>there are data sets for which the compatibility
>criterion is as good or better than parsimony.
>The property
>that such data would have to have is that each
>state of each character would arise with such low
>probability that perforce the states would occupy
>subtrees.  Genomic rearrangements, for example, might
>be one such property.  ANy thoughts on this?

I looked into this in two papers: 1979 in Systematic Zoology, and 1981 in
Biological Journal of the Linnean Society.  If each state arises with very
low probability BOTH parsimony and compatibility will do well.  The
condition for compatibility to do well is that rates of evolution vary
widely between characters, being low for most characters and high for a
small minority.  That way when a character is interpreted as having any
noise, one can more or less ignore its information, though you want to do
so to as few characters as possible.  (I am using the word "character" in
the sense of a site, not of a derived state).

Presumably "political" issues aside, the reason compatibility is less
widely used is that most systematists or molecular evolutionists feel
that the noisy characters still contain a lot of information.

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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