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Molecular Biology and Evolution 17:469-473 (2000)
© 2000 Society for Molecular Biology and Evolution

Regular Articles

Phylogeny Reconstruction Using Duplicate Genes

Mark P. Simmons2,, C. Donovan Bailey and Kevin C. Nixon

L. H. Bailey Hortorium, Cornell University

Abstract

In this paper, we propose a new method (uninode coding) for coding duplicate (paralogous) genes to infer species trees. Uninode coding incorporates data from duplicated and unduplicated gene copies in phylogenetic analyses of taxa. Uninode coding utilizes global parsimony through the inclusion of both duplicated and unduplicated gene copies, allows one to code all data sources from a taxon into a single terminal, and overcomes problems of character dependence among duplicated and unduplicated gene copies. We present an example of uninode coding using the phytochrome A and phytochrome C data from a study by Donoghue and Mathews.


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