Preface…
Table of Contents…
Contributing Authors…
Part I Evolutionary Timescales
1. Dating Microbial Evolution with MCMCtree
Mario dos Reis
2. A Computational Protocol for Dating the Evolution of Cyanobacteria
Hao Zhang, Sishuo Wang, and Haiwei Luo
3. Standard Candles for Dating Microbial Lineages
Gregory P. Fournier, Chris W. Parsons, Emilie M. Cutts, and Erik Tamre
4. Relative Time Inference using Lateral Gene Transfers
Adrián A. Davín, Dominik Schrempf, Tom A. Williams, Philip Hugenholtz, and Gergely J. Szöllosi
5. Estimating the Divergence Times of Alphaproteobacteria Based on Endosymbiosis and Eukaryotic Fossils
Sishuo Wang and Haiwei Luo
Part II Deep Phylogeny
6. Phylogenetic Analysis that Models Compositional Heterogeneity Over the Tree
Peter G. Foster
7. Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies
Qiyun Zhu and Siavash Mirarab
8. Testing Phylogenetic Stability with Variable Taxon Sampling
Christopher Lowell Edward Powell and Fabia Ursula Battistuzzi
9. Rooting Species Trees using Gene Tree-Species Tree Reconciliation
Brogan J. Harris, Paul O. Sheridan, Adrián A. Davín, Cecile Gubry-Rangin, Gergely J. Szöllosi, and Tom A. Williams
10. Reconstructing Gene Gains and Losses with Badirate
Pablo Librado and Julio Rozas
11. Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL
Mukul S. Bansal
Part III Trait Evolution
12. Ancestral State Reconstruction using BayesTraits
Andrew Meade and Mark Pagel
13. An Integrated Method to Reconstruct Ancient Proteins
Amanda K. Garcia, Evrim Fer, Cathryn Sephus, and Betul Kacar
14. Methodologies for Microbial Ancestral Sequence Reconstruction
Miguel Arenas
15. Reconstruction of State-Dependent Diversification: Integrating Phenotyping Traits into Molecular Phylogenies
Leonel Herrera-Alsina, Poppy Mynard, I. Made Sudiana, Berry Juliandi, Justin M.J. Travis, and Cécile Gubry-Rangin
16. Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model
Takao K. Suzuki, Motomu Matsui, Sira Sriswasdi, and Wataru Iwasaki
17. Assessing a Role of Genetic Drift for Deep-Time Evolutionary Events
Xiaoyuan Feng, Hao Zhang, Jijun Tang, and Haiwei Luo
Subject Index List…
