Estimating Species Trees Practical and Theoretical Aspects

, by Knowles, L. Lacey; Kubatko, Laura S.

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ISBN: 9780470526859 | 0470526858
Cover: Hardcover
Copyright: 9/22/2010

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Recent computational and modeling advances have produced methods for estimating species trees directly, avoiding the problems and limitations of the traditional phylogenetic paradigm where an estimated gene tree is equated with the history of species divergence. The overarching goal of the volume is to increase the visibility and use of these new methods by the entire phylogenetic community by specifically addressing several challenges: (i) firm understanding of the theoretical underpinnings of the methodology, (ii) empirical examples demonstrating the utility of the methodology as well as its limitations, and (iii) attention to technical aspects involved in the actual software implementation of the methodology. As such, this volume will not only be poised to become the quintessential guide to training the next generation of researchers, but it will also be instrumental in ushering in a new phylogenetic paradigm for the 21 st century.

Preface
Contributors
Estimating Species Trees: An Introduction To Concepts and Models
Introduction
Different Tree Types and Their Relationship to Phylogeny
The Relationship Between Gene Trees and Species Trees
Evolutionary Mechanisms for Gene Tree Discord
The Coalescent Process and Gene Tree Distributions
Phylogenetic Extensions of the Coalescent Model
The Relationship Between Sequence Data and Gene Trees
Modeling DNA Sequence Evolution along a Gene Tree
Statistical Inference of Species Trees
ML
Bayesian Analysis
Collecting DNA Sequence Data
Conclusions
References
Bayesian Estimation Of Species Trees: A Practical Guide To Optimal Sampling and Analysis
Introduction
Empirical Examples Using BEST
Factors Influencing Confidence in Estimated Species Trees Using BEST
Simulation Protocol
Results of Simulations on Number and Length of Loci
Multifactorial Prediction of Confidence in Species Trees
Effect of the Number of Alleles Sampled per Locus on Species Tree Estimation
Effect of Recombination on Species Tree Inference
Some Tips on Running the BEST MCMC Algorithm
Conclusions and Challenges
Acknowledgments
References
Reconstructing Concordance Trees and Testing The Coalescent Model From Genome-Wide Data Sets
Introduction
BCA: Background
Sharing of Information across Gene Trees
How to Choose the A Priori Level of Discordance ¿
The Choice of an Infinite ¿in BCA
A Nonparametric Prior Distribution on Gene Trees
Genomic Support versus Statistical Support
Comparing CFs of Contradicting Clades for Reconstructing the Dominant History
Testing the Hypothesis That All Discordance Is Due to ILS
Species Tree Reconstruction From CFs
The Challenge of Determining Loci on Whole-Genome Alignments
The Assumption of Homogeneous, Unlinked Loci for GT/ST Reconstruction
Detecting Recombination Breakpoints for GT/ST Reconstruction
A Minimum Description Length (MDL) Information Criterion
Comparisons with Other Partitioning Criteria
Acknowledgments
References
Probabilities of Gene Tree Topologies With Intraspecific Sampling Given A Species Tree
Introduction
Background and Terminology
Incomplete Lineage Sorting
Notation
Gene Tree Topology Probabilities-Theory
Enumerating Coalescent Histories
The Probability of a Coalescent History
Probability Mass Function for Gene Tree Topologies
Gene Tree Topology Probabilities-Examples
Enumeration of Coalescent Histories
Calculation of Probabilities of Coalescent Histories
Applications
Probabilities of Multilabeled Trees
Probability of Monophyletic Concordance
AGTs
Conclusions
References
Appendix: Using Coal
Using the Software
Setting Up Species Tree Branch Lengths
Inference Of Parsimonious Species Tree from Multilocus Data By Minimizing Deep Coalescences
Introduction
Trees, Clusters, and The Compatibility Graph
Valid Coalescent Histories, Extra Lineages, and The MDC Criterion
Exact Algorithms for The MDC Problem
An ILP Algorithm
A DP Algorithm
Handling Special Cases
Multiple Individuals per Species
Nonbinary Trees
Performance of MDC
Inference from The Clusters of The Gene Trees
Using PhyloNet
Using PhyloNet to Count Valid Coalescent Histories
Using PhyloNet to Infer Species Trees Under MDC
Conclusions
Acknowledgments
References
Accommodating Hybridization in A Multilocus Phylogenetic Framework
Introduction
Methods for Detecting Hybridization in The Presence of Incomplete Lineage Sorting
A Phylogenetic Model for Hybridization in The Presence of Incomplete Lineage Sorting
Estimation and Testing for the Hybridization Parameters: Gene Tree Data
Estimation and Testing for the Hybridization Parameters: Sequence Data
Comparison of Hybrid Species Phylogenies Using Gene Tree Data
Application: Hybridization in the Heliconius Butterflies
Estimation and Testing for the Hybridization Parameters: Application to the Estimated Gene Trees in Heliconius
Estimation and Testing for the Hybridization Parameters: Application to Sequence Data in Heliconius
Comparison of Hybrid Species Phylogenies for the Heliconius Gene Tree Data
Conclusions and Future Directions
Acknowledgment
References
The Influence of Hybrid Zones On Species Tree Inference in Manakins
Introduction
The Manacus Manakins
Distribution
Hybrid Zone between M. vitellinus and M. candei
Two Contact Zones between M. vitellinus and M. manacus
Inferring a Manacus Species Tree
Is Introgression Across the Hybrid Zones Influencing the Species Tree Inference?
Conclusions
Acknowledgments
References
Summarizing Gene Tree Incongruence At Multiple Phylogenetic Depths
Introduction
Sample Data: Rice, Flies, and Yeast
Bayesian Inference of Gene Trees
Detecting Convergence Across Hundreds of Genes
A Note on Combining Trees
BCA
gsi
Triplet Analysis
Missing Data
Genomic Distribution of Gene Tree Incongruence
Visualization of Gene Tree Incongruence
Concluding Remarks
Acknowledgments
References
Species Tree Estimation for Complex Divergence Histories: A Case Study In Neodiprion Sawflies
Introduction
Study System: Neodiprion Sawflies
Sampling Strategy
Determining the Source of Mitonuclear Discordance
Approaches for Species Tree Estimation
Concatenation with Monophyly Constraints (CMC)
Minimize Deep Coalescences (MDC)
Shallowest Divergences (SD)
Bayesian Estimation of Species Trees (BEST)
Comparison of Species Tree Estimates
Comparison of Gene Trees to Species Trees
Conclusions and Future Directions
References
Sampling Strategies for Species Tree Estimation
Introduction
Information Content in DNA Sequences for Species Tree Inference
Why Phylogenetic History Dictates Appropriate Sampling Strategy
Properties of the Data That Impact Sampling Decisions
Making Informed Decisions about Sampling Strategies
Where Does the Initial Species Tree Come from?
Is There Consistency in the Estimated Species Tree Given the Data?
Summary
Acknowledgments
References
Developing Nuclear Sequences for Species Tree Estimation in Nonmodel Organisms: Insights from A Case Study of Bottae's Pocket Gopher, Thomomys Bottae
Introduction
Pocket Gophers
Marker Generation Approach and Methodological Comments
Library Construction
Subtraction of High-Copy-Number Regions
Locus Characterization by Genomic Approaches
Primer Design Experiments
Locus Evaluation for Inclusion in the Study
Variation within the Library Construction Species
Inclusion of Loci and Data Generation within the Genus
Data Management and Analysis
Handling Data and Choosing Analysis Programs
Phylogenetic Analysis
Conclusions
Acknowledgments
References
Estimating Species Relationships and Taxon Distinctiveness in Sistrurus Rattlesnakes Using Multilocus Data
Introduction
Sistrurus Rattlesnakes
Analysis of Species and Subspecific Relationships
Estimation of the Species Phylogeny
Distinctiveness of Subspecies
Phased versus Unphased Data
Species Tree Estimation
Estimation Using Gene Trees as Data
Estimation Using Sequences as Data
Distinctiveness Among Species and Subspecies
Phased Data
Unphased Data and the Effect of Sample Size
Evolutionary and Conservation Implications
Conclusions
Acknowledgments
References
Index
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Estimating Species Trees Practical and Theoretical Aspects

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