Character weighting

Hennig86 was written by James S. Farris (American Museum of Natural History, New York, NY 10024). It is a fast and effective parsimony program. It is often faster than PAUP but has many fewer features and options. However, Hennig86 does contain a routine for successive approximation a posteriori character weighting. 

This condition produces long branch attraction —the long branches become artihcially connected because the number of nonhomologous similarities the sequences have accumulated exceeds the number of homologous similarities they have retained with their true closest relatives (Swofford et al 1996). Character weighting improves the performance of MP under these conditions (Huelsenbeck, 1995). 

Farris (1990) pointed out that his program Hennig-86 uses an updated successive approximations approach which includes a corrected homoplasy index. The original index was shown to be biased by the number of taxa and number of characters used in a study (Archie, 1989a, Farris 1989). The revised homoplasy measure used, called the "retention index", is the same as Archie s "homoplasy excess ratio maximum" (Archie 1990, Farris 1990), which is an estimator of the "homoplasy excess ratio" used in his test of character state randomness (Archie 1989ab). The consistency index for individual characters can be rescaled to vary between zero and one by multiplying it by the retention index and this value can be used for character weighting (Farris 1990, Archie 1990). 

Farris JS (1969) A successive approximations approach to character weighting. Syst Zool 18 374-385... 

Kluge, A.G., Sophisticated falsification and research cycles consequences for differential character weighting in phylogenetic systematics, ZooL Scripta, 26, 349-360, 1997. 

Numerical a priori character weighting and its theoretical justification... 

If valid means of character weighting can be found, they will tend to improve our chances of inferring the correct phylogeny. (Kluge and Farris, 1969)... 

FFennig did weigh characters, but in a simple way, by excluding some from the analysis (weight 0) and including others (weight 1). In the meantime, several methods for differentiated character weighting have been proposed. I do not intend to discuss all the criteria but will concentrate on some basic theoretical considerations. 

The discussion between cladists and their critics is not new. Panchen reviewed the issues in 1982 (Panchen, 1982). He attacked the restriction to just parsimony, by the optimization of synapomorphies of cladograms, and pointed out that in the real world parallel evolution is common. What he did not offer was a theory that allows the classification of characters into those that are predisposed to parallelism or chance similarity and those that are not, and therefore he thought that cladists may have to admit the persistent intuitive element in classification. Today, intuition (in the sense of unfounded ad hoc assumptions) can be avoided in phylogenetic cladistics using objective criteria of character weighting. 

Bryant, H.N., An evaluation of cladistic and character analyses as hypothetico-deductive procedures, and the consequences for character weighting, Syst. Zool., 38, 214-227, 1989. 

Goloboff, P.A., Estimating character weights during tree search, Cladistics, 9, 83-91, 1993. 

Haszprunar, G., Parsimony analysis as a specific kind of homology estimation and the implications for character weighting. Mol. Phylogenet. Evol, 9, 333—339, 1998. 

Sharkey, M.J., A hypothesis-independent method of character weighting for cladistic analysis, Cladistics, 5, 63-86, 1989. 

Wheeler, Q.D., Character weighting and cladistic analysis, Syst. Zool., 35, 102-109, 1986. 

Recent advances in numerical taxonomy including character weighting and evolutionary interpretations. Developments in phenetic classification of hominids and other groups. Nature of characters and biological significance of correlation [Pg.182]

A Theoretical Basis for a priori Character Weighting Discussion... 

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