Who are your closest relatives? Algorithms for reconciling non-binary species trees
While reconciling a binary gene tree with a binary species tree is a well-studied, tractable problem, the standard reconciliation algorithm yields incorrect results when applied to non-binary species trees. Binary reconciliation makes simplifying assumptions about genetic variation in ancestral populations that are not justified when the species tree is non-binary. We present the first formal algorithms for reconciling binary gene trees with non-binary species trees. Our algorithms, which combine models from standard reconciliation and population genetics, have been implemented in Notung, a free, publicly available software tool available at http://www.cs.cmu.edu/~durand/Notung. I will discuss the application of these methods to resolving uncertainty in species trees, with examples from species lineages that are currently debated in the evolutionary biology literature.