Trees in the Presence of Polymorphic Characters

Most phylogenetics literature and construction methods based upon characters presume monomorphism (one state per character per species), and yet polymorphism (multiple states per character per species) is well documented in both Biology and Historical Linguistics. In this paper we consider the problem of inferring evolutionary trees for polymorphic characters. We show effieient algorithms for the construction of perfect phylogenies from polymorphic data. These methods have been used to help construct the evolutionary tree proposed by Warnow, Ringe, and Taylor for the Indo-European family of languages, which was presented by invitation at the National Academy of Sciences in November

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