Constructing level-2 phylogenetic networks from triplets

Authors:
Leo Van Iersel;Judith Keijsper;Steven Kelk;Leen Stougie;Ferry Hagen;Teun Boekhout
Affiliations:
Department of Mathematics and Computer Science, Technische Universiteit Eindhoven, Eindhoven, The Netherlands;Department of Mathematics and Computer Science, Technische Universiteit Eindhoven, Eindhoven, The Netherlands;Centrum voor Wiskunde en Informatica, Amsterdam, The Netherlands;Department of Mathematics and Computer Science, Technische Universiteit Eindhoven, Eindhoven, The Netherlands and Centrum voor Wiskunde en Informatica, Amsterdam, The Netherlands;Centraalbureau voor Schimmelcultures, Fungal Biodiversity Center, Utrecht, The Netherlands;Centraalbureau voor Schimmelcultures, Fungal Biodiversity Center, Utrecht, The Netherlands
Venue:
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Year:
2008

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Abstract

Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so to construct such a network [18]. Here we extend this work by showing that this problem is even polynomial-time solvable for the construction of level-2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily non-tree like. This further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data.