Cover
Contents
Preface
Acknowledgments
List of Contributors
Chapter 1. Introduction to Species Tree Inference
1.1 Introduction
1.2 Background and Terminology
1.2.1 Definitions and Terminology
1.2.2 An Introduction to the Multispecies Coalescent
1.2.3 Data Types and Technologies for Generating Phylogenomic Data
1.3 Overview of Current Methods for Species Tree Inference
1.3.1 Controversies in the Estimation of Species Trees
1.4 A Look to the Future
1.4.1 Current Limitations and Future Prospects
1.4.2 Beyond the Species Tree
1.5 Organization of This Book
Part I. Analytical and Methodological Developments
Chapter 2. Large-Scale Species Tree Estimation
2.1 Introduction
2.2 Species Tree Estimation Methods Addressing ILS
2.2.1 Overview
2.2.2 Summary Methods
2.2.3 Coestimation Methods
2.2.4 Site Based Methods
2.2.5 Evaluation of Branch Support in Species Trees
2.3 Species Tree Estimation under GDL
2.4 Parallel Implementations for Species Tree Estimation
2.4.1 ASTRAL-MP
2.4.2 Multilocus Species Tree Estimation Using Maximum Likelihood
2.5 Divide-and-Conquer Species Tree Estimation
2.5.1 Divide-and-Conquer Using Supertree Methods
2.5.2 Divide-and-Conquer Using Disjoint Tree Merger Methods
2.6 Choice of Method
2.6.1 Statistical Consistency
2.6.2 Empirical Performance
2.7 Summary, Challenges, and Future Directions
2.8 Appendix: Big-O Analysis
Chapter 3. Species Tree Estimation Using ASTRAL: Practical Considerations
3.1 Introduction
3.2 ASTRAL Algorithm
3.2.1 Motivation and History
3.2.2 ASTRAL Algorithm
3.2.3 Summary of Known Theoretical Results Related to ASTRAL
3.3 Accuracy
3.4 Running Time
3.5 Input to ASTRAL: Practical Considerations
3.5.1 Gene Tree Estimation
3.5.2 Filtering of Data
3.6 ASTRAL Output
3.6.1 Species Tree Topology and Its Quartet Score
3.6.2 Branch Lengths in Coalescent Units
3.6.3 Branch Support Using Local Posterior Probability (localPP)
3.7 Follow-up Analyses and Visualization
3.7.1 Tests for Polytomies
3.7.2 Per Branch Quartet Support (Measure of Discordance)
3.8 Conclusion
Chapter 4. Species Tree Estimation Using Site Pattern Frequencies
4.1 Introduction
4.2 Estimation of the Species Tree Topology Using SVDQuartets
4.2.1 Theoretical Basis
4.2.2 Accounting of Incomplete Lineage Sorting in SVDQuartets
4.2.3 Species Tree Inference: Quartet Sampling and Assembly
4.2.4 Algorithmic Details
4.2.5 Uncertainty Quantification
4.2.6 Application to Species Relationships among Gibbons
4.2.7 Properties of SVDQuartets
4.2.8 Recommendations for Using SVDQuartets
4.3 Estimation of Speciation Times
4.3.1 Theoretical Basis
4.3.2 Algorithmic Details
4.3.3 Uncertainty Quantification
4.3.4 Application to Species Relationships among Gibbons
4.3.5 Recommendations for Using Composite Likelihood Estimators of the Speciation Times
4.4 Conclusion and Future Work
Chapter 5. Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
5.1 Introduction
5.2 Reading and Interpretation of a Phylogenetic Network
5.2.1 Phylogenetic Network Parameters and Their Identifiability
5.3 Heuristic Searches, Point Estimates, and Posterior Distributions, or, Why Am I Getting Different Networks in Different Runs?
5.4 Illustration of the Various Inference Methods in PhyloNet
5.4.1 Inference under the MDC Criterion
5.4.2 Maximum Likelihood Inference
5.4.3 Maximum Pseudolikelihood Inference
5.4.4 Bayesian Inference
5.4.5 Running Time
5.5 Analysis of Larger Data Sets
5.6 Comparison and Summarization of Networks
5.6.1 Displayed Trees
5.6.2 Backbone Networks
5.6.3 Tree Decompositions
5.6.4 Tripartitions
5.6.5 Major Trees
5.7 Reticulate Evolutionary Processes in PhyloNet
5.7.1 Analysis of Polyploids
5.8 Conclusions
Notes
Chapter 6. Network Thinking: Novel Inference Tools and Scalability Challenges
6.1 Introduction: The Impact of Gene Glow
6.2 Trees versus Networks
6.3 Species Networks
6.3.1 Explicit versus Implicit Networks
6.3.2 Extended Parenthetical Format
6.3.3 Displayed Trees and Subnetworks
6.3.4 Comparison of Networks
6.4 Fast Reconstruction of Species Networks
6.4.1 Maximum Pseudolikelihood Estimation
6.4.2 Rooting of Semidirected Networks
6.4.3 Goodness of Fit Tools
6.4.4 Bootstrap Analysis
6.5 Appendix: Installation and Use of the PhyloNetworks Julia Package
6.5.1 Main Functions in PhyloNetworks
Part II. Empirical Inference
Chapter 7. Phylogenomic Conflict in Plants
7.1 Introduction
7.2 Two Examples of Gene Tree Conflict within Angiosperms
7.3 The Consequences of Gene Tree Conflict in Phylogenomics
7.3.1 Inference of Species Trees
7.3.2 Gene Duplication and Genome Duplication
7.3.3 Divergence Time and Comparative Analyses
7.4 Resolution of the Tree of Plant Life
Chapter 8. Hybridization in Iochroma
8.1 Introduction
8.2 Methods
8.2.1 Study System
8.2.2 Experimental Design
8.2.3 Target Capture and Assembly
8.2.4 Detection of Patterns of Hybridization from Gene Tree Distributions
8.2.5 Testing of Hybridization in Empirical Data Sets
8.3 Results
8.3.1 Addition of Hybrid Taxa Increases Discordance and Decreases Tree-Like Signal
8.3.2 Tests of Hybridization Support Different Relationships than Expected
8.4 Discussion
8.4.1 Effects of Hybridization on Patterns of Gene Tree Discordance
8.4.2 Challenges in Determining the Exact Hybrid Relationships
8.4.3 Hybridization in Iochrominae
8.5 Conclusions
Chapter 9. Hybridization and Polyploidy in Penstemon
9.1 Introduction
9.2 Approach
9.2.1 Calculation of Quartet Concordance Factors
9.2.2 Bootstrapping and Gene Tree Uncertainty
9.2.3 Validation of QCF Estimation
9.2.4 Implementation
9.3 Materials and Methods
9.3.1 Study System
9.3.2 Sample Collection, DNA Extraction, and Amplicon Sequencing
9.3.3 Species Tree Inference
9.3.4 Candidate Hybridization Events from Rooted Triples
9.3.5 Species Network Inference
9.4 Results
9.4.1 Nuclear Amplicon Data
9.4.2 Species Tree Inference
9.4.3 Tests for Hybridization and Species Network Inference
9.5 Discussion
9.5.1 Taxonomy of Subsections Humiles and Proceri
9.5.2 Character Evolution and Biogeography
9.5.3 Phylogenetics of Hybrids and Polyploids
9.6 Conclusions
Chapter 10. Comparison of Linked versus Unlinked Character Models for Species Tree Inference
10.1 Introduction
10.2 Methods
10.2.1 Simulations of Error-Free Data Sets
10.2.2 Introduction of Site Pattern Errors
10.2.3 Assessment of Sensitivity to Errors
10.2.4 Project Repository
10.3 Results
10.3.1 Behavior of Linked (StarBEAST2) versus Unlinked (Ecoevolity) Character Models
10.3.2 Analysis of All Sites versus SNPs with Ecoevolity
10.3.3 Coverage of Credible Intervals
10.3.4 MCMC Convergence and Mixing
10.4 Discussion
10.4.1 Robustness to Character-Pattern Errors
10.4.2 Relevance to Empirical Data Sets
10.4.3 Recommendations for Using Unlinked-Character Models
10.4.4 Other Complexities of Empirical Data in Need of Exploration
Part III. Beyond the Species Tree
Chapter 11. The Unfinished Synthesis of Comparative Genomics and Phylogenetics: Examples from Flightless Birds
11.1 Introduction
11.1.1 Phylogenetics of Modern Birds
11.1.2 Paleognathous Birds as a Test Case for Post-Genomic Phylogenetics
11.2 Building of a Whole-Genome Species Tree for an Ancient Radiation of Birds
11.3 The Unfinished Synthesis of Comparative Genomics and Genomic Heterogeneity
11.3.1 A Species Tree for Paleognathous Birds as a Foundation for Comparative Genomics
11.3.2 Accommodation of Uncertainty into Whole-Genome Alignments
11.3.3 Gene Tree Heterogeneity and Detecting Rate Variation in Genes and Noncoding Regions
11.3.4 Phylogenetic Analysis of Quantitative βOmics Data: Gene Expression and Epigenetics
11.4 Conclusions
Chapter 12. Phylogenetic Analysis under Heterogeneity and Discordance
12.1 Introduction
12.2 The Origin of Discordance
12.2.1 A History of Systems and Methods
12.2.2 Concepts of Harmony and Discordance
12.2.3 The Species Tree
12.2.4 Comparison of the Incomparable
12.3 Characterization and Quantification of Phylogenetic Heterogeneity
12.3.1 Quantification and Visualization of Discordance
12.3.2 Quantification of Conflict and Tree Evaluation
12.3.3 Visualization of Conflict
12.4 Analysis under Phylogenetic Heterogeneity
12.4.1 Testing of Introgression and Hybridization under Phylogenetic Heterogeneity
12.4.2 Testing of Selection under Phylogenetic Heterogeneity
12.4.3 Testing of Traits under Phylogenetic Heterogeneity
12.4.4 Testing of Coevolution under Phylogenetic Heterogeneity
12.5 Conclusion
Chapter 13. The Multispecies Coalescent in Space and Time
13.1 Introduction
13.2 Coalescent Simulations
13.2.1 Units, Space, and Time
13.2.2 Tree Size, Tree Space, and Phylogenetic Decay
13.3 Linked Genealogies and Gene Tree Inference
13.4 Conclusions
Chapter 14. Tree Set Visualization, Exploration, and Applications
14.1 Introduction to Visualizing and Exploring Tree Sets
14.1.1 Tree Set Visualization
14.1.2 Detection of Structure in Tree Sets
14.2 Applications to Gene Trees, Species Trees, and Phylogenomics
14.2.1 Sensitivity to Models of Sequence Evolution
14.2.2 Joint versus Independent Inference of Gene Trees
14.2.3 Understanding of Variation across Genomes
14.2.4 Prospects for Future Development and Application
14.3 Appendix
Bibliography
Index