Environmental Microbial Evolution: Methods and Protocols (Hardcover) (ISBN-13: 9781071626900)

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
Adri疣 A. Dav匤, Dominik Schrempf, Tom A. Williams, Philip Hugenholtz, and Gergely J. Szlősi

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, Adri疣 A. Dav匤, Cecile Gubry-Rangin, Gergely J. Szlősi, 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 C馗ile 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...

Author: Haiwei Luo
ISBN-10: 1071626906
ISBN-13: 9781071626900
Publisher: Humana
Language: English
Published: 09/10/2022
Pages: 362
Format: Hardcover
Weight: 1.91lbs
Size: 10.00h x 7.00w x 0.88d