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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.
Evolutionary Timescales
Dating Microbial Evolution with MCMCtree
A Computational Protocol for Dating the Evolution of Cyanobacteria
Standard Candles for Dating Microbial Lineages
Relative Time Inference Using Lateral Gene Transfers
Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils
Deep Phylogeny
Phylogenetic Analysis That Models Compositional Heterogeneity over the Tree
Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies
Testing Phylogenetic Stability with Variable Taxon Sampling
Rooting Species Trees Using Gene Tree-Species Tree Reconciliation
Reconstructing Gene Gains and Losses with BadiRate
Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL
Trait Evolution
Ancestral State Reconstruction Using BayesTraits
An Integrated Method to Reconstruct Ancient Proteins
Methodologies for Microbial Ancestral Sequence Reconstruction
Reconstruction of State-Dependent Diversification: Integrating Phenotypic Traits into Molecular Phylogenies
Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model
Assessing a Role of Genetic Drift for Deep-Time Evolutionary Events