Polytomy refinement for the correction of dubious duplications in gene trees

Abstract

Motivation: Large-scale methods for inferring gene trees are errorprone. Correcting gene trees for weakly supported features often results in non-binary trees, i.e. trees with polytomies, thus raising the natural question of refining such polytomies into binary trees. A feature pointing toward potential errors in gene trees are duplications that are not supported by the presence of multiple gene copies. Results: We introduce the problem of refining polytomies in a gene tree whileminimizing the number of created non-Apparent duplications in the resulting tree. We show that this problem can be described as a graph-Theoretical optimization problem. We provide a bounded heuristic with guaranteed optimality for well-characterized instances. We apply our algorithm to a set of ray-finned fish gene trees from the Ensembl database to illustrate its ability to correct dubious duplications.. © The Author(s) 2014.