Species tree inference : a guide to methods and applications

Species tree inference : a guide to methods and applications /

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Bibliographic Details
Corporate Author: ProQuest (Firm)
Other Authors: Kubatko, Laura S. (Laura Salter) (Editor), Knowles, L. Lacey (Editor)
Format: Electronic eBook
Language:English
Published: Princeton : Princeton University Press, [2023]
Subjects:
Phylogeny.
Biology > Classification.
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.

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