Estimating Species Trees: Practical and Theoretical Aspects Book

Preface

Contributors

Chapter 1 Estimating Species Trees: An Introduction to Concepts and Models Laura S. Kubatko Kubatko, Laura S. 1

1.1 Introduction 1

1.1.1 Different Tree Types and Their Relationship to Phylogeny 1

1.2 The Relationship Between Gene Trees and Species Trees 3

1.2.1 Evolutionary Mechanisms for Gene Tree Discord 4

1.2.2 The Coalescent Process and Gene Tree Distributions 5

1.2.3 Phylogenetic Extensions of the Coalescent Model 7

1.3 The Relationship Between Sequence Data and Gene Trees 8

1.3.1 Modeling DNA Sequence Evolution along a Gene Tree 8

1.4 Statistical Inference of Species Trees 8

1.4.1 ML 9

1.4.2 Bayesian Analysis 10

1.5 Collecting DNA Sequence Data 11

1.6 Conclusions 12

References 12

Chapter 2 Bayesian Estimation of Species Trees: A Practical Guide to Optimal Sampling and Analysis Scott V. Edwards Edwards, Scott V. 15

2.1 Introduction 15

2.1.1 Empirical Examples Using BEST 17

2.2 Factors Influencing Confidence in Estimated Species Trees Using BEST 17

2.2.1 Simulation Protocol 18

2.2.2 Results of Simulations on Number and Length of Loci 20

2.2.3 Multifactorial Prediction of Confidence in Species Trees 22

2.2.4 Effect of the Number of Alleles Sampled per Locus on Species Tree Estimation 23

2.2.5 Effect of Recombination on Species Tree Inference 25

2.3 Some Tips on Running the BEST MCMC Algorithm 26

2.4 Conclusions and Challenges 30

Acknowledgments 31

References 32

Chapter 3 Reconstructing Concordance Trees and Testing The Coalescent Model From Genome-Wide Data Sets Cecile Ane Ane, Cecile 35

3.1 Introduction 35

3.2 BCA: Background 36

3.2.1 Sharing of Information across Gene Trees 36

3.2.2 How to Choose the A Priori Level of Discordance α 37

3.2.3 The Choice of an Infinite α in BCA 37

3.2.4 A Nonparametric Prior Distribution on Gene Trees 38

3.3 Genomic Support versus Statistical Support 38

3.4 Comparing CFs of Contradicting Clades for Reconstructing the Dominant History 41

3.5 Testing the Hypothesis That All Discordance is Due to ILS 43

3.6 Species Tree Reconstruction From CFs 45

3.7 The Challenge of Determining Loci on Whole-Genome Alignments 47

3.7.1 The Assumption of Homogeneous, Unlinked Loci for GT/ST Reconstruction 47

3.7.2 Detecting Recombination Breakpoints for GT/ST Reconstruction 47

3.7.3 A Minimum Description Length (MDL) Information Criterion 49

3.7.4 Comparisons with Other Partitioning Criteria 50

Acknowledgments 50

References 51

Chapter 4 Probabilities of Gene Tree Topologies with Intraspecific Sampling Given A Species Tree James H. Degnan Degnan, James H. 53

4.1 Introduction 53

4.2 Background and Terminology 54

4.2.1 Incomplete Lineage Sorting 54

4.2.2 Notation 56

4.3 Gene Tree Topology Probabilities---Theory 56

4.3.1 Enumerating Coalescent Histories 58

4.3.2 The Probability of a Coalescent History 59

4.3.3 Probability Mass Function for Gene Tree Topologies 61

4.4 Gene Tree Topology Probabilities---Examples 62

4.4.1 Enumeration of Coalescent Histories 62

4.4.2 Calculation of Probabilities of Coalescent Histories 64

4.5 Applications 65

4.5.1 Probabilities of Multilabeled Trees 65

4.5.2 Probability of Monophyletic Concordance 68

4.5.3 AGTs 70

4.6 Conclusions 73

References 73

Appendix: Using Coal 75

Using the Software 75

Setting Up Species Tree Branch Lengths 76

Chapter 5 Inference of Parsimonious Species Tree From Multilocus Data By Minimizing Deep Coalescences Luay Nakhleh Nakhleh, Luay 79

5.1 Introduction 79

5.2 Trees, Clusters, and The Compatibility Graph 80

5.3 Valid Coalescent Histories, Extra Lineages, and the MDC Criterion 82

5.4 Exact Algorithms for The MDC Problem 84

5.4.1 An ILP Algorithm 85

5.4.2 A DP Algorithm 86

5.5 Handling Special Cases 87

5.5.1 Multiple Individuals per Species 87

5.5.2 Nonbinary Trees 88

5.6 Performance of MDC 89

5.7 Inference from The Clusters of the Gene Trees 91

5.8 Using PhyloNet 94

5.8.1 Using PhyloNet to Count Valid Coalescent Histories 94

5.8.2 Using PhyloNet to Infer Species Trees Under MDC 95

5.9 Conclusions 96

Acknowledgments 96

References 96

Chapter 6 Accommodating Hybridization in a Multilocus Phylogenetic Framework Chen Meng Chen, Meng 99

6.1 Introduction 99

6.2 Methods for Detecting Hybridization in The Presence of Incomplete Lineage Sorting 100

6.3 A Phylogenetic Model for Hybridization in The Presence of Incomplete Lineage Sorting 101

6.3.1 Estimation and Testing for the Hybridization Parameters: Gene Tree Data 104

6.3.2 Estimation and Testing for the Hybridization Parameters: Sequence Data 106

6.3.3 Comparison of Hybrid Species Phylogenies Using Gene Tree Data 107

6.4 Application: Hybridization in the Heliconius Butterflies 108

6.4.1 Estimation and Testing for the Hybridization Parameters: Application to the Estimated Gene Trees in Heliconius 109

6.4.2 Estimation and Testing for the Hybridization Parameters: Application to Sequence Data in Heliconius 109

6.4.3 Comparison of Hybrid Species Phylogenies for the Heliconius Gene Tree Data 111

6.5 Conclusions and Future Directions 112

Acknowledgment 112

References 113

Chapter 7 The Influence of Hybrid Zones on Species Tree Inference in Manakins Matthew D. Carling Carling, Matthew D. 115

7.1 Introduction 115

7.2 The Manacus Manakins 117

7.2.1 Distribution 117

7.2.2 Hybrid Zone between M. Candei Candei, M. 118

7.2.3 Two Contact Zones between M. Manacus Manacus, M. 119

7.2.4 Inferring a Manacus Species Tree 121

7.3 Is Introgression Across the Hybrid Zones Influencing the Species Tree Inference? 123

7.4 Conclusions 125

Acknowledgments 126

References 126

Chapter 8 Summarizing Gene Tree Incongruence At Multiple Phylogenetic Depths Karen A. Cranston Cranston, Karen A. 129

8.1 Introduction 129

8.2 Sample Data: Rice, Flies, and Yeast 130

8.3 Bayesian Inference of Gene Trees 132

8.4 Detecting Convergence Across Hundreds of Genes 132

8.5 A Note on Combining Trees 134

8.6 BCA 134

8.7 gsi 136

8.8 Triplet Analysis 137

8.9 Missing Data 139

8.10 Genomic Distribution of Gene Tree Incongruence 139

8.11 Visualization of Gene Tree Incongruence 140

8.12 Concluding Remarks 141

Acknowledgments 141

References 142

Chapter 9 Species Tree Estimation For Complex Divergence Histories: A Case Study in Neodiprion Sawflies Catherine R. Linnen Linnen, Catherine R. 145

9.1 Introduction 145

9.2 Study System: Neodiprion Sawflies 146

9.3 Sampling Strategy 147

9.4 Determining the Source of Mitonuclear Discordance 147

9.5 Approaches for Species Tree Estimation 150

9.5.1 Concatenation with Monophyly Constraints (CMC) 151

9.5.2 Minimize Deep Coalescences (MDC) 152

9.5.3 Shallowest Divergences (SD) 152

9.5.4 Bayesian Estimation of Species Trees (BEST) 154

9.6 Comparison of Species Tree Estimates 156

9.7 Comparison of Gene Trees to Species Trees 158

9.8 Conclusions and Future Directions 158

References 160

Chapter 10 Sampling Strategies For Species Tree Estimation L. Lacey Knowles Knowles, L. Lacey 163

10.1 Introduction 163

10.2 Information Content in DNA Sequences for Species Tree Inference 163

10.3 Why Phylogenetic History Dictates Appropriate Sampling Strategy 166

10.4 Properties of the Data That Impact Sampling Decisions 168

10.5 Making Informed Decisions about Sampling Strategies 169

10.5.1 Where Does the Initial Species Tree Come from? 169

10.5.2 Is There Consistency in the Estimated Species Tree Given the Data? 170

10.6 Summary 172

Acknowledgments 172

References 172

Chapter 11 Developing Nuclear Sequences For Species Tree Estimation in Nonmodel Organisms: Insights From A Case Study of Bottae's Pocket Gopher, Thomomys Bottae Natalia M. Belfiore Belfiore, Natalia M. 175

11.1 Introduction 175

11.2 Pocket Gophers 176

11.3 Marker Generation Approach and Methodological Comments 176

11.3.1 Library Construction 177

11.3.2 Subtraction of High-Copy-Number Regions 178

11.3.3 Locus Characterization by Genomic Approaches 180

11.3.4 Primer Design Experiments 180

11.3.5 Locus Evaluation for Inclusion in the Study 181

11.3.6 Variation within the Library Construction Species 182

11.3.7 Inclusion of Loci and Data Generation within the Genus 186

11.4 Data Management and Analysis 186

11.4.1 Handling Data and Choosing Analysis Programs 186

11.4.2 Phylogenetic Analysis 187

11.5 Conclusions 189

Acknowledgments 190

References 190

Chapter 12 Estimating Species Relationships and Taxon Distinctiveness in Sistrurus Rattlesnakes Using Multilocus Data H. Lisle Gibbs Gibbs, H. Lisle 193

12.1 Introduction 193

12.1.1 Sistrurus Rattlesnakes 194

12.2 Analysis of Species and Subspecific Relationships 194

12.2.1 Estimation of the Species Phylogeny 195

12.2.2 Distinctiveness of Subspecies 198

12.2.3 Phased versus Unphased Data 199

12.3 Species Tree Estimation 200

12.3.1 Estimation Using Gene Trees as Data 200

12.3.2 Estimation Using Sequences as Data 201

12.4 Distinctiveness Among Species and Subspecies 203

12.4.1 Phased Data 203

12.4.2 Unphased Data and the Effect of Sample Size 204

12.5 Evolutionary and Conservation Implications 205

12.6 Conclusions 205

Acknowledgments 206

References 206

Index 209