Reconstructing evolutionary trees – Chances and pitfalls in modern phylogenetics

From CRCG-Wiki

Ever since Darwin published his first sketch of an evolutionary tree in 1859, scientists have been trying to reconstruct the ‘Tree of Life’. Such reconstructions are nowadays usually based on DNA data, which is interpreted with the help of tree inference methods. Maximum Parsimony (MP), Maximum Likelihood (ML) and distance-based methods (DB) are three such methods which are frequently used. In the first part of my talk, I will introduce MP and DB and I will show that even for the best possible DNA data, these methods can give contradictory results. In the second part of my talk, I will focus on the relationship between MP and ML, which has been widely discussed. For instance, it is well known that under a simple model of substitution, MP and ML always choose the same set of trees for DNA sequences. But some surprising properties of MP and ML have only recently been discovered: I will present examples for MP and ML favoring different trees when the underlying model is changed slightly – for example, when substitution probabilities are subject to an upper bound or when a molecular clock condition is imposed. Finally, I will show that, even though the two parts of my talk may seem unrelated at first glance, the same construction idea can be used to establish both results.

This talk is based on joint work with Bhalchandra Thatte and Hans-Jürgen Bandelt.