Phylogeny: Discrete and Random Processes in Evolution

Description

Preface ix Acknowledgments xi Commonly Used Symbols xiii 1 Phylogeny 1 1.1 What is phylogenetics? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 Phylogenetic trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2 Basic combinatorics of discrete phylogenies 15 2.1 Counting trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2.2 Rooted trees as nested sets of clusters . . . . . . . . . . . . . . . . . . . . . 18 2.3 Refinement, compatibility, and encoding . . . . . . . . . . . . . . . . . . . 21 2.4 Unrooted trees as systems of splits . . . . . . . . . . . . . . . . . . . . . . . 23 2.5 Tree rearrangement metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 2.6 Consensus functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 3 Tree shape and random discrete phylogenies 41 3.1 Tree shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 3.2 The shape of evolving trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 3.3 Measuring and modeling tree shape . . . . . . . . . . . . . . . . . . . . . . 53 3.4 Cherries and extended Pólya urn models . . . . . . . . . . . . . . . . . . . 58 4 Pulling trees apart and putting trees together 63 4.1 Restriction and display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 4.2 When is a collection of trees compatible? . . . . . . . . . . . . . . . . . . . 67 4.3 Sets of trees that “define” and “identify” a phylogeny . . . . . . . . . . . 72 4.4 Agreement subtrees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 4.5 Phylogenetic decisiveness and terraces . . . . . . . . . . . . . . . . . . . . . 82 5 Phylogenies based on discrete characters 87 5.1 Characters, homoplasy, and perfect phylogeny . . . . . . . . . . . . . . . 87 5.2 Minimal evolution (maximum parsimony (MP)) . . . . . . . . . . . . . . 100 5.3 Minimal evolution trees for a sequence of characters . . . . . . . . . . . 107 6 Continuous phylogenies and distance-based tree reconstruction 111 6.1 Metrics from trees with edge lengths. . . . . . . . . . . . . . . . . . . . . . 111 6.2 Distance-based tree reconstruction methods . . . . . . . . . . . . . . . . . 121 6.3 Generalizations and geometry . . . . . . . . . . . . . . . . . . . . . . . . . . 129 6.4 Phylogenetic diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 7 Evolution on a tree: Part one 147 7.1 Nonhomogeneous Markov chains . . . . . . . . . . . . . . . . . . . . . . . 148 7.2 From Markov chains to processes on trees . . . . . . . . . . . . . . . . . . 153 7.3 Classes and properties of models . . . . . . . . . . . . . . . . . . . . . . . . 157 7.4 The Hadamard story . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 7.5 Phylogenetic mixture models . . . . . . . . . . . . . . . . . . . . . . . . . . 171 8 Evolution on a tree: Part two 177 8.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 8.2 Phylogeny reconstruction methods and properties . . . . . . . . . . . . 180 8.3 Algebraic analysis of Markov models . . . . . . . . . . . . . . . . . . . . . 191 8.4 The infinite-state random cluster model . . . . . . . . . . . . . . . . . . . 197 8.5 Additional topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203 9 Evolution of trees 205 9.1 Yule pure-birth trees: The simplest model . . . . . . . . . . . . . . . . . . 206 9.2 Birth-death models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211 9.3 Gene trees and species trees . . . . . . . . . . . . . . . . . . . . . . . . . . . 224 10 Introduction to phylogenetic networks 237 10.1 To tree or not to tree: Why networks? . . . . . . . . . . . . . . . . . . . . 237 10.2 Implicit (unrooted) networks . . . . . . . . . . . . . . . . . . . . . . . . . . 238 10.3 Explicit (directed) networks . . . . . . . . . . . . . . . . . . . . . . . . . . . 245 10.4 Trees displayed by networks . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 10.5 Reconstructing networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261 10.6 Additional topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267 Bibliography 269 Index 291