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A Framework for Representing Reticulate Evolution
Mihaela Baroni1, Charles Semple2, and Mike Steel3
Biomathematics Research Centre, Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
mbaroni@ugal.ro, {c.semple, m.steel}@math.canterbury.ac.nz
Annals of Combinatorics 8 (4) p.391-408 December, 2004
AMS Subject Classification: 05C05, 92D15
Abstract:
Acyclic directed graphs (ADGs) are increasingly being viewed as more appropriate for representing certain evolutionary relationships, particularly in biology, than rooted trees. In this paper, we develop a framework for the analysis of these graphs which we call hybrid phylogenies. We are particularly interested in the problem whereby one is given a set of phylogenetic trees and wishes to determine a hybrid phylogeny that `embeds' each of these trees and which requires the smallest number of hybridisation events. We show that this quantity can be greatly reduced if additional species are involved, and investigate other combinatorial aspects of this and related questions.
Keywords: directed acyclic graph, reticulate evolution, hybrid species, subtree prune and regraft

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