Estimating species trees : practical and theoretical aspects

摘要: Preface. Contributors. Chapter 1 Estimating Species Trees: An Introduction to Concepts and Models (L. Lacey Knowles Laura S. Kubatko). 1.1 Introduction. 1.1.1 Different Tree Types Their Relationship Phylogeny. 1.2 The Between Gene Trees Trees. 1.2.1 Evolutionary Mechanisms for Discord. 1.2.2 Coalescent Process Distributions. 1.2.3 Phylogenetic Extensions of the Model. 1.3 Sequence Data 1.3.1 Modeling DNA Evolution along a Tree. 1.4 Statistical Inference 1.4.1 ML. 1.4.2 Bayesian Analysis. 1.5 Collecting Data. 1.6 Conclusions. References. 2 Estimation A Practical Guide Optimal Sampling Analysis (Santiago Castillo-Ramirez, Liang Liu, Dennis Pearl Scott V. Edwards). 2.1 2.1.1 Empirical Examples Using BEST. 2.2 Factors Influencing Confidence in Estimated 2.2.1 Simulation Protocol. 2.2.2 Results Simulations on Number Length Loci. 2.2.3 Multifactorial Prediction 2.2.4 Effect Alleles Sampled per Locus Estimation. 2.2.5 Recombination Inference. 2.3 Some Tips Running BEST MCMC Algorithm. 2.4 Conclusions Challenges. Acknowledgments. 3 Reconstructing Concordance Testing Model from Genome-Wide Sets (Cecile Ane). 3.1 3.2 BCA: Background. 3.2.1 Sharing Information across 3.2.2 How Choose Priori Level Discordance alpha. 3.2.3 Choice an Infinite alpha BCA. 3.2.4 Nonparametric Prior Distribution 3.3 Genomic Support versus Support. 3.4 Comparing CFs Contradicting Clades Dominant History. 3.5 Hypothesis That All is Due ILS. 3.6 Reconstruction CFs. 3.7 Challenge Determining Loci Whole-Genome Alignments. 3.7.1 Assumption Homogeneous, Unlinked GT/ST Reconstruction. 3.7.2 Detecting Breakpoints 3.7.3 Minimum Description (MDL) Criterion. 3.7.4 Comparisons with Other Partitioning Criteria. 4 Probabilities Topoligies Intraspecific Given (James H. Degnan). 4.1 4.2 Background Terminology. 4.2.1 Incomplete Lineage Sorting. 4.2.2 Notation. 4.3 Topology Probabilities-Theory. 4.3.1 Enumerating Histories. 4.3.2 Probability 4.3.3 Mass Function Topologies. 4.4 Probabilities-Examples. 4.4.1 Enumeration 4.4.2 Calculation 4.5 Applications. 4.5.1 Multilabeled 4.5.2 Monophyletic Concordance. 4.5.3 AGTs. 4.6 Appendix: Coal. Software. Setting Up Branch Lengths. 5 Parsimonious Multilocus by Minimizing Deep Coalescences (Cuong Than Luay Nakhleh). 5.1 5.2 Trees, Clusters, Compatibility Graph. 5.3 Valid Histories, Extra Lineages, MDC 5.4 Exact Algorithms Problem. 5.4.1 ILP 5.4.2 DP 5.5 Handling Special Cases. 5.5.1 Multiple Individuals Species. 5.5.2 Nonbinary 5.6 Performance MDC. 5.7 Clusters 5.8 PhyloNet. 5.8.1 PhyloNet Count 5.8.2 Infer Under 5.9 6 Accommodating Hybridization Framework (Laura Kubatko Chen Meng). 6.1 6.2 Methods Presence 6.3 6.3.1 Parameters: 6.3.2 6.3.3 Comparison Hybrid Phylogenies 6.4 Application: Heliconius Butterflies. 6.4.1 Application Heliconius. 6.4.2 6.4.3 6.5 Future Directions. Acknowledgment. 7 Influence Zones Manakins (Robb T. Brumfi eld Matthew D. Carling). 7.1 7.2 Manacus Manakins. 7.2.1 Distribution. 7.2.2 Zone between M. vitellinus candei. 7.2.3 Two Contact manacus. 7.2.4 Inferring 7.3 Is Introgression Across Inference? 7.4 8 Summarizing Incongruence at Depths (Karen A. Cranston). 8.1 8.2 Sample Data: Rice, Flies, Yeast. 8.3 8.4 Convergence Hundreds Genes. 8.5 Note Combining 8.6 8.7 gsi. 8.8 Triplet 8.9 Missing 8.10 Incongruence. 8.11 Visualization 8.12 Concluding Remarks. 9 Complex Divergence Histories: Case Study Neodiprion Sawflies (Catherine R. Linnen). 9.1 9.2 System: Sawflies. 9.3 Strategy. 9.4 Source Mitonuclear Discordance. 9.5 Approaches 9.5.1 Concatenation Monophyly Constraints (CMC). 9.5.2 Minimize (MDC). 9.5.3 Shallowest Divergences (SD). 9.5.4 (BEST). 9.6 Estimates. 9.7 9.8 10 Strategies Knowles). 10.1 10.2 Content Sequences 10.3 Why History Dictates Appropriate 10.4 Properties Impact Decisions. 10.5 Making Informed Decisions about Strategies. 10.5.1 Where Does Initial Come from? 10.5.2 There Consistency Data? 10.6 Summary. 11 Developing Nuclear Nonmodel Organisms: Insights Bottae's Pocket Gopher, Thomomys Bottae (Natalia Belfiore). 11.1 11.2 Gophers. 11.3 Marker Generation Approach Methodological Comments. 11.3.1 Library Construction. 11.3.2 Subtraction High-Copy-Number Regions. 11.3.3 Characterization Approaches. 11.3.4 Primer Design Experiments. 11.3.5 Evaluation Inclusion Study. 11.3.6 Variation within Construction 11.3.7 Genus. 11.4 Management 11.4.1 Choosing Programs. 11.4.2 11.5 12 Relationships Taxon Distinctiveness Sistrurus Rattlesnakes Lisle Gibbs). 12.1 12.1.1 Rattlesnakes. 12.2 Subspecific Relationships. 12.2.1 12.2.2 Subspecies. 12.2.3 Phased Unphased 12.3 12.3.1 as 12.3.2 12.4 Among 12.4.1 12.4.2 Size. 12.5 Conservation Implications. 12.6 Index.