Evaluation of ultrametric phylogenetic tree estimation

다국어 초록 (Multilingual Abstract)

A phylogenetic tree is a tree-like graphical representation of the evolutionary history of a group of organisms. An ultrametric tree is a phylogenetic tree scaled to time, which is estimated from DNA sequences of the organisms. PAUP* is a popular software used to estimate diverse types of phylogenetic trees including ultrametric trees. An ultrametric tree includes the lengths of edges which are the major parameters of interest, and PAUP* provides three ways to parameterize the edge lengths. In this work, analyses of simulated and real data were conducted to examine the performance of ultrametric tree estimations by PAUP*. The three parameterizations, called relAge, Thorne, and Rambaut, were found to be correctly estimated in most cases, although the relAge parameterization resulted in tree estimation with zero-length branches less often than others. The Rambaut parameterization had higher accuracy in the tree structure estimation in the simulation.

목차 (Table of Contents)

• Abstract
• 1. Introduction
• 2. Statistical evolutionary models
• 3. Simulation study
• 4. Real data analysis
• 5. Conclusion
• References