[Taxacom] SINES, LINES and chromosomal rearrangements

[Sergio Vargas]

  Hi,

just a brief comment on compatibility.

Compatibility was originally proposed by Lequesne in Syst. Zool. 1969 (A 
METHOD OF SELECTION OF CHARACTERS IN NUMERICAL TAXONOMY), later 
developed by other authors, and finally quasi-destroyed by Felsenstein 
in Syst. Zool. 1978 (CASES IN WHICH PARSIMONY OR COMPATIBILITY METHODS 
WILL BE POSITIVELY MISLEADING). Some use the principle to find 
generalized tracks in panbiogeography.

It is not exactly the same thing as finding a tree that maximizes 
congruence because one only tries to find the maximum number of 
compatible characters using a clique algorithm for this. First a 
compatibility matrix is calculated and this matrix (interpreted as a 
graph) is use to find the largest clique of compatible characters. The 
result is a set of fully compatible characters that imply a tree with 
100% CI. The logic would be: maximize compatibility first and then 
deduce the tree. If you don't use this, you search for the tree that 
maximizes congruence of the entire matrix, i.e. including homoplasic 
characters. During optimization solutions that minimize (globally) the 
number of steps will be favored. If compatibility is used, homoplasic 
characters are simply not used, even if they could potentially add 
structure to the phylogenetic tree.

sergio

On 5/6/11 7:00 PM, taxacom-request at mailman.nhm.ku.edu wrote:
> Perhaps it's my ignorance, but picking the largest set of mutually
> congruent characters seems like it's effectively the same thing as a
> 'tree'. But then I admit my ignorance of the clique analysis algorithm
> and accept I could be wrong in that assertion.
>
> John Grehan