Supertree Methods for Ancestral Divergence Dates and other Applications

Abstract

There are many ways to combine rooted phylogenetic trees with overlapping leaf sets into a single “supertree”. The most widely used method is MRP (matrix representation with parsimony analysis), but other direct methods have been developed recently. However, all these methods utilize typically only the discrete topology of the input trees and ignore other information that might be available. Based, for example, on fossil data or molecular dating techniques, this information includes whether one particular divergence event occurred earlier or later than another, and actual time estimates for divergence events. The ability to include such information in supertree construction could allow for more accurate dating of certain species divergences. This is a topical problem in recent biological literature. In this chapter, we describe a way to incorporate divergence time information in a fast and exact supertree algorithm that extends the classic Build algorithm. The approach is somewhat flexible in that it allows any combination of relative and/or absolute divergence times. In addition to this extension, the last section of this chapter consists of applications of Build to problems in phylogenetics that are, in general, computationally challenging.