A Study on Tree-Like Phylogenetic Networks: Reconstruction and Encodings

• Main Authors: Chang, Kuang-Yu, 張光瑜
• Other Authors: Hon, Wing-Kai
• Format: Others
• Language: en_US
• Published: 2019
• Online Access: http://ndltd.ncl.edu.tw/handle/hj3dsb

博士 === 國立清華大學 === 資訊工程學系所 === 107 === A phylogenetic network is a directed acyclic graph for representing the evolutionary history between species or taxa involving reticulation events. Here, we focus on two classes of phylogenetic networks: 1-articulated networks and galled trees (level-1 networks). Since these networks contain only a small number of additional edges from their embedded spanning tree, we refer to them as tree-like networks. Two main problems are discussed in the dissertation: The first one is to reconstruct 1-articulated networks from distance matrices, which represent the evolutionary distance between species. Our main result is a O(n^2) time algorithm, where n is the number of species, for constructing networks where the shortest evolutionary path between any pair of species satisfies the input distance. The other is to encode a level-1 network. For this problem, we propose a compact encoding, and show that the tree containment with galled tree can be solved optimally with our encoding. Other related problems are also discussed in this dissertation. The problems include the \emph{tree containing problem} (TCP) for 1-articulated networks, reconstructing 1-articulated networks from set-distance matrices, and reconstructing 2-articulated networks from distance matrices.