Measuring how far a nonbinary phylogenetic network is from being tree-based

Measuring how far a nonbinary phylogenetic network is from being tree-based

Janisse, Frank (TU Delft Electrical Engineering, Mathematics and Computer Science)

van Iersel, Leo (mentor)

Delft University of Technology

2018-01-29

In computational biology, phylogenetic trees are used to describe evolutionary history. This can be done more generally using phylogenetic networks, which can also describe nontreelike events such as hybridization. Some phylogenetic networks can be obtained from a base tree, a rooted spanning tree with the same leaf set, by adding linking edges. Such networks are called tree-based. In recent articles, characterizations of binary tree-based networks are given. They are linked to maximum-sized matchings in bipartite graphs, path partitions and antichains. However, in many real-life applications, phylogenetic networks are not binary. Therefore, we will prove that some characterizations are extendable to all (nonbinary) phylogenetic networks while some others are not. We will discuss five proximity measures of how close an arbitrarily (nonbinary) phylogenetic network is to being tree-based. Three of the measures turn out to be equal and at least three of them are computable in polynomial time. We show that this is also true in the nonbinary case. Lastly, we prove two inequalities comparing the other measures.

Phylogenetic network
Tree-based
Deviation
Binary
Nonbinary

http://resolver.tudelft.nl/uuid:961c6a92-1d6e-4bfd-b8db-7ff4fa3694fa

Student theses

bachelor thesis

© 2018 Frank Janisse