Species tree inference : a guide to methods and applications /
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Format: | Electronic eBook |
Language: | English |
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Princeton :
Princeton University Press,
[2023]
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Online Access: | Connect to this title online (unlimited simultaneous users allowed; 325 uses per year) |
Table of Contents:
- Machine generated contents note: ch. 1 Introduction to Species Tree Inference
- 1.1. Introduction
- 1.2. Background and Terminology
- 1.2.1. Definitions and Terminology
- 1.2.2. 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. 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
- pt. I Analytical and Methodological Developments
- ch. 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
- ch. 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
- ch. 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
- ch. 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
- ch. 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
- pt. II Empirical Inference
- ch. 7 Phylogenomic Conflict in Plants
- 7.1. Introduction
- 7.2. Two Examples of Gene Tree Conflict within Angiosperms
- 7.3. 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
- ch. 8 Hybridization in lochroma
- 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 lochrominae
- 8.5. Conclusions
- ch. 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
- ch. 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
- pt. III Beyond the Species Tree
- ch. 11 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. Unfinished Synthesis of Comparative Genomics and Genomic Heterogeneity
- 11.3.1. 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 `Omics Data: Gene Expression and Epigenetics'
- 11.4. Conclusions
- ch. 12 Phylogenetic Analysis under Heterogeneity and Discordance
- 12.1. Introduction
- 12.2. Origin of Discordance
- 12.2.1. History of Systems and Methods
- 12.2.2. Concepts of Harmony and Discordance
- 12.2.3. 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
- ch. 13 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
- ch. 14 Tree Set Visualization, Exploration, and Applications
- Contents note continued: 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.