Albrecht, Benjamin (2016): Computing hybridization networks using agreement forests. Dissertation, LMU München: Faculty of Mathematics, Computer Science and Statistics 

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Abstract
Rooted phylogenetic trees are widely used in biology to represent the evolutionary history of certain species. Usually, such a tree is a simple binary tree only containing internal nodes of indegree one and outdegree two representing specific speciation events. In applied phylogenetics, however, trees can contain nodes of outdegree larger than two because, often, in order to resolve some orderings of speciation events, there is only insufficient information available and the common way to model this uncertainty is to use nonbinary nodes (i.e., nodes of outdegree of at least three), also denoted as polytomies. Moreover, in addition to such speciation events, there exist certain biological events that cannot be modeled by a tree and, thus, require the more general concept of rooted phylogenetic networks or, more specifically, of hybridization networks. Examples for such reticulate events are horizontal gene transfer, hybridization, and recombination. Nevertheless, in order to construct hybridization networks, the less general concept of a phylogenetic tree can still be used as building block. More precisely, often, in a first step, phylogenetic trees for a set of species, each based on a distinctive orthologous gene, are constructed. In a second step, specific sets containing common subtrees of those trees, known as maximum acyclic agreement forests, are calculated, which are then glued together to a single hybridization network. In such a network, hybridization nodes (i.e., nodes of indegree larger than or equal to two) can exist representing potential reticulate events of the underlying evolutionary history. As such events are considered as rare phenomena, from a biological point of view, especially those networks representing a minimum number of reticulate events, which is denoted as hybridization number, are of high interest. Consequently, in a mathematical aspect, the problem of calculating hybridization networks can be briefly described as follows. Given a set T of rooted phylogenetic trees sharing the same set of taxa, compute a hybridization network N displaying T with minimum hybridization number. In this context, we say that such a network N displays a phylogenetic tree T, if we can obtain T from N by removing as well as contracting some of its nodes and edges. Unfortunately, this is a computational hard problem (i.e., it is NPhard), even for the simplest case given just two binary input trees. In this thesis, we present several methods tackling this NPhard problem. Our first approach describes how to compute a representative set of minimum hybridization networks for two binary input trees. For that purpose, our approach implements the first nonnaive algorithm  called allMAAFs  calculating all maximum acyclic agreement forests for two rooted binary phylogenetic trees on the same set of taxa. In a subsequent step, in order to maximize the efficiency of the algorithm allMAAFs, we have developed additionally several modifications each reducing the number of computational steps and, thus, significantly improving its practical runtime. Our second approach is an extension of our first approach making the underlying algorithm accessible to more than two binary input trees. For this purpose, our approach implements the algorithm allHNetworks being the first algorithm calculating all relevant hybridization networks displaying a set of rooted binary phylogenetic trees on the same set of taxa, which is a preferable feature when studying hybridization events. Lastly, we have developed a generalization of our second approach that can now deal with multiple nonbinary input trees. For that purpose, our approach implements the first nonnaive algorithm  called allMulMAAFs  calculating a relevant set of nonbinary maximum acyclic agreement forests for two rooted (nonbinary) phylogenetic trees on the same set of taxa. Each of the algorithms above is integrated into our user friendly Javabased software package Hybroscale, which is freely available and platform independent, so that it runs on all major operating systems. Our program provides a graphical user interface for visualizing trees and networks. Moreover, it facilitates the interpretation of computed hybridization networks by adding specific features to its graphical representation and, thus, supports biologists in investigating reticulate evolution. In addition, we have implemented a method using a user friendly SQLstyle modeling language for filtering the usually large amount of reported networks.
Item Type:  Theses (Dissertation, LMU Munich) 

Keywords:  hybridization networks, maximum acyclic agreement forests, phylogenetics 
Subjects:  000 Computers, Information and General Reference > 004 Data processing computer science 500 Natural sciences and mathematics > 570 Life sciences 
Faculties:  Faculty of Mathematics, Computer Science and Statistics 
Language:  English 
Date of oral examination:  8. April 2016 
1. Referee:  Heun, Volker 
MD5 Checksum of the PDFfile:  fc2dd604519845dae123c0a73b2b626c 
Signature of the printed copy:  0001/UMC 23794 
ID Code:  19444 
Deposited On:  24. May 2016 11:33 
Last Modified:  30. Oct 2020 13:39 