Title: Effects of rooting via out-groups on in-group topology in phylogeny

Authors: Margareta Ackerman; Daniel G. Brown; David Loker

Addresses: Department of Computer Science and Engineering, University of California, San Diego La Jolla, CA, USA ' Cheriton School of Computer Science, Waterloo, Ontario, Canada ' Cheriton School of Computer Science, Waterloo, Ontario, Canada

Abstract: Users of phylogenetic methods require rooted trees, because the direction of time depends on the placement of the root. While phylogenetic trees are typically rooted by using an out-group, this mechanism is inappropriate when the addition of an out-group changes the in-group topology. We perform a formal analysis of phylogenetic algorithms under the inclusion of distant out-groups. It turns out that linkage-based algorithms (including UPGMA) and a class of bisecting methods do not modify the topology of the in-group when an out-group is included. By contrast, the popular neighbour joining algorithm fails this property in a strong sense: every data set can have its structure destroyed by some arbitrarily distant outlier. Furthermore, including multiple outliers can lead to an arbitrary topology on the in-group. The standard rooting approach that uses out-groups may be fundamentally unsuited for neighbour joining.

Keywords: phylogeny; rooting; UPGA; neighbour joining; out-groups; in-group topology; phylogenetic trees; bioinformatics.

DOI: 10.1504/IJBRA.2014.062993

International Journal of Bioinformatics Research and Applications, 2014 Vol.10 No.4/5, pp.426 - 446

Published online: 24 Oct 2014 *

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