
Species Tree Inference
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Content
- 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 'Omics 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
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