Species Tree Inference: A Guide to Methods and Applications

• Publisher: Princeton University Press
• Year: 2023
• Tongue: English
• Leaves: 352
• Category: Library

✦ Synopsis

An up-to-date reference book on phylogenetic methods and applications for evolutionary biologists

The increasingly widespread availability of genomic data is transforming how biologists estimate evolutionary relationships among organisms and broadening the range of questions that researchers can test in a phylogenetic framework. Species Tree Inference brings together many of today’s leading scholars in the field to provide an incisive guide to the latest practices for analyzing multilocus sequence data.

This wide-ranging and authoritative book gives detailed explanations of emerging new approaches and assesses their strengths and challenges, offering an invaluable context for gauging which procedure to apply given the types of genomic data and processes that contribute to differences in the patterns of inheritance across loci. It demonstrates how to apply these approaches using empirical studies that span a range of taxa, timeframes of diversification, and processes that cause the evolutionary history of genes across genomes to differ.

By fully embracing this genomic heterogeneity, Species Tree Inference illustrates how to address questions beyond the goal of estimating phylogenetic relationships of organisms, enabling students and researchers to pursue their own research in statistically sophisticated ways while charting new directions of scientific discovery.

✦ Table of Contents

Short Contents
Preface
Acknowledgments
Contributors
CHAPTER 1 Introduction to Species Tree Inference
PART I Analytical and Methodological Developments
Introduction
CHAPTER 2 Large-Scale Species Tree Estimation
CHAPTER 3 Species Tree Estimation Using ASTRAL: Practical Considerations
CHAPTER 4 Species Tree Estimation Using Site Pattern Frequencies
CHAPTER 5 Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
CHAPTER 6 Network Thinking: Novel Inference Tools and Scalability Challenges
PART II Empirical Inference
Introduction
CHAPTER 7 Phylogenomic Conflict in Plants
CHAPTER 8 Hybridization in Iochroma
CHAPTER 9 Hybridization and Polyploidy in Penstemon
CHAPTER 10 Comparison of Linked versus Unlinked Character Models for Species Tree Inference
PART III Beyond the Species Tree
Introduction
CHAPTER 11 The Unfinished Synthesis of Comparative Genomics and Phylogenetics: Examples from Flightless Birds
CHAPTER 12 Phylogenetic Analysis under Heterogeneity and Discordance
CHAPTER 13 The Multispecies Coalescent in Space and Time
CHAPTER 14 Tree Set Visualization, Exploration, and Applications
Bibliography
Index