Inferring Phylogenetic Trees Using Answer Set Programming

Authors:
Daniel R. Brooks;Esra Erdem;Selim T. Erdoğan;James W. Minett;Don Ringe
Affiliations:
Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada;Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey;Department of Computer Sciences, University of Texas at Austin, Austin, USA;Department of Electronic Engineering, Chinese University of Hong Kong, Shatin, Hong Kong;Department of Linguistics, University of Pennsylvania, Philadelphia, USA
Venue:
Journal of Automated Reasoning
Year:
2007

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Abstract

We describe the reconstruction of a phylogeny for a set of taxa, with a character-based cladistics approach, in a declarative knowledge representation formalism, and show how to use computational methods of answer set programming to generate conjectures about the evolution of the given taxa. We have applied this computational method in two domains: historical analysis of languages and historical analysis of parasite-host systems. In particular, using this method, we have computed some plausible phylogenies for Chinese dialects, for Indo-European language groups, and for Alcataenia species. Some of these plausible phylogenies are different from the ones computed by other software. Using this method, we can easily describe domain-specific information (e.g., temporal and geographical constraints), and thus prevent the reconstruction of some phylogenies that are not plausible.