Reconciling Gene Trees with Apparent Polytomies

Abstract

<p>We consider the problem of reconciling gene trees with a species tree based on the widely accepted Gene Duplication model from Goodman <em>et al</em>. Current algorithms that solve this problem handle only binary gene trees or interpret polytomies in the gene tree as true. While in practice polytomies occur frequently, they are typically not true. Most polytomies represent unresolved evolutionary relationships. In this case a polytomy is called <em>apparent</em>. In this work, we modify the problem of reconciling gene and species trees by interpreting polytomies to be apparent, based on a natural extension of the Gene Duplication model. We further provide polynomial time algorithms to solve this modified problem.</p>