title: Effects of rooting via out-groups on in-group topology in phylogeny.
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.
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego La Jolla, CA, USA.
authors.forename: Margareta
authors.initials: M
authors.lastname: Ackerman
authors.affiliation: Cheriton School of Computer Science, Waterloo, Ontario, Canada.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Brown
authors.affiliation: Cheriton School of Computer Science, Waterloo, Ontario, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Loker
mesh_terms: D000465:Algorithms; D000818:Animals; D001516:Bees / Q000145:classification; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D015233:Models, Statistical; D010802:Phylogeny; D012624:Seaweed / Q000145:classification; D012984:Software
keywords: UPGA; bioinformatics; in–group topology; neighbour joining; out–groups; phylogenetic trees; phylogeny; rooting