Skip to main content
Springer Nature Link
Log in

Environmental Microbial Evolution

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Haiwei Luo

    1. School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2569)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

About this book

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.
 


Similar content being viewed by others

Keywords

Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Evolutionary Timescales

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Dating Microbial Evolution with MCMCtree

      • Mario dos Reis
      Pages 3-22

    3. A Computational Protocol for Dating the Evolution of Cyanobacteria

      • Hao Zhang, Sishuo Wang, Haiwei Luo
      Pages 23-40

    4. Standard Candles for Dating Microbial Lineages

      • Gregory P. Fournier, Chris W. Parsons, Elise M. Cutts, Erik Tamre
      Pages 41-74

    5. Relative Time Inference Using Lateral Gene Transfers

      • Adrián A. Davín, Dominik Schrempf, Tom A. Williams, Philip Hugenholtz, Gergely J. Szöllősi
      Pages 75-94

    6. Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils

      • Sishuo Wang, Haiwei Luo
      Pages 95-116

  3. Deep Phylogeny

    1. Front Matter

      Pages 117-117
      Download chapter PDF

    2. Phylogenetic Analysis That Models Compositional Heterogeneity over the Tree

      • Peter G. Foster
      Pages 119-135

    3. Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies

      • Qiyun Zhu, Siavash Mirarab
      Pages 137-165

    4. Testing Phylogenetic Stability with Variable Taxon Sampling

      • Christopher Lowell Edward Powell, Fabia Ursula Battistuzzi
      Pages 167-188

    5. Rooting Species Trees Using Gene Tree-Species Tree Reconciliation

      • Brogan J. Harris, Paul O. Sheridan, Adrián A. Davín, Cécile Gubry-Rangin, Gergely J. Szöllősi, Tom A. Williams
      Pages 189-211

    6. Reconstructing Gene Gains and Losses with BadiRate

      • Pablo Librado, Julio Rozas
      Pages 213-232

    7. Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL

      • Mukul S. Bansal
      Pages 233-252

  4. Trait Evolution

    1. Front Matter

      Pages 253-253
      Download chapter PDF

    2. Ancestral State Reconstruction Using BayesTraits

      • Andrew Meade, Mark Pagel
      Pages 255-266

    3. An Integrated Method to Reconstruct Ancient Proteins

      • Amanda K. Garcia, Evrim Fer, Cathryn Sephus, Betul Kacar
      Pages 267-281

    4. Methodologies for Microbial Ancestral Sequence Reconstruction

      • Miguel Arenas
      Pages 283-303

    5. Reconstruction of State-Dependent Diversification: Integrating Phenotypic Traits into Molecular Phylogenies

      • Leonel Herrera-Alsina, Poppy Mynard, I. Made Sudiana, Berry Juliandi, Justin M. J. Travis, Cécile Gubry-Rangin
      Pages 305-326

    6. Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model

      • Takao K. Suzuki, Motomu Matsui, Sira Sriswasdi, Wataru Iwasaki
      Pages 327-342
Back to top

Editors and Affiliations

  • School of Life Sciences, Earth and Environmental Sciences Programme, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China

    Haiwei Luo

Bibliographic Information

  • Book Title: Environmental Microbial Evolution

  • Book Subtitle: Methods and Protocols

  • Editors: Haiwei Luo

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2691-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2690-0Published: 10 September 2022

  • Softcover ISBN: 978-1-0716-2693-1Published: 11 September 2023

  • eBook ISBN: 978-1-0716-2691-7Published: 09 September 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 362

  • Number of Illustrations: 20 b/w illustrations, 58 illustrations in colour

  • Topics: Microbiology

Publish with us

Policies and ethics

Back to top