Environmental Microbial Evolution

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 Endosymbiosis and Eukaryotic Fossils.- 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.- Ancestral State Reconstruction using BayesTraits.- An Integrated Method to Reconstruct Ancient Proteins.- Methodologies for Microbial Ancestral Sequence Reconstruction.- Reconstruction of State-Dependent Diversification: Integrating Phenotyping 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.