Environmental Microbial Evolution: Methods and Protocols

ISBN-13: 9781071626900 / Angielski / Twarda / 2022

Luo, Haiwei

Opis

This volume explores the latest techniques used to study environmental microbial evolution, with a focus on methods capable of addressing deep evolution at long timescales. The chapters in this book are organized into three parts. Part One introduces molecular dating approaches and time calibration ideas that allow for the determination of evolutionary timescales of microbial lineages. Part Two describes several advanced phylogenomic tools such as models for genome tree construction, a taxon sampling method, outgroup-independent tree-rooting methods, and gene family evolution models. Part Three covers techniques used to study trait evolution. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Environmental Microbial Evolution: Methods and Protocols is a valuable tool for all researchers who are interested in learning more about this important and evolving field.

 

Spis treści

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. Szöllősi

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. Szöllősi, 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…