1 Introduction to Species Tree Inference / L. Lacey Knowles and Laura S. Kubatko
PART I ANALYTICAL AND METHODOLOGICALDEVELOPMENTS
2 Large-Scale Species Tree Estimation / Erin Molloy and Tandy Warnow
3 Species Tree Estimation Using ASTRAL:Practical Considerations / Siavash Mirarab
4 Species Tree Estimation Using SitePattern Frequencies / David L. Swofford and Laura S. Kubatko
5 Practical Aspects of Phylogenetic Network AnalysisUsing PhyloNet / Zhen Cao, Xinhao Liu, Huw A. Ogilvie, Zhi Yan, and Luay Nakhleh
6 Network Thinking: Novel Inference Toolsand Scalability Challenges / Claudia Sol̕s-Lemus
PART II Empirical Inference
7 Phylogenomic Conflict in Plants / Joseph F. Walker and Stephen A. Smith
8 Hybridization in Iochroma / Daniel J. Gates, Diana Pilson, and Stacey D. Smith
9 Hybridization and Polyploidy in Penstemon / Paul D. Blischak, Coleen E. Thompson, Emiko M. Waight,Laura S. Kubatko, and Andrea D. Wolfe
10 Comparison of Linked versus Unlinked CharacterModels for Species Tree Inference / Kerry Cobb and Jamie R. Oaks
PART III Beyond the Species Tree
11 The Unfinished Synthesis of ComparativeGenomics and Phylogenetics: Examples fromFlightless Birds / Alexandria A. DiGiacomo, Alison Cloutier, Phil Grayson, Timothy B. Sackton,and Scott V. Edwards
12 Phylogenetic Analysis under Heterogeneityand Discordance / James B. Pease and Ellen I. Weinheimer
13 The Multispecies Coalescent in Space and Time / Patrick F. McKenzie and Deren A. R. Eaton
14 Tree Set Visualization, Exploration, and Applications / Jeremy M. Brown, Genevieve G. Mount, Kyle A. Gallivan, and James C. Wilgenbusch