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Titlebook: Environmental Microbial Evolution; Methods and Protocol Haiwei Luo Book 2022 The Editor(s) (if applicable) and The Author(s), under exclusi

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Phylogenetic Analysis That Models Compositional Heterogeneity over the Treemodels of evolution in common use are homogeneous over the tree, and if used in a phylogenetic analysis with compositionally tree-heterogeneous datasets these models can recover incorrect trees. The NDCH or Node-Discrete Compositional Heterogeneity model is able to model such data by accommodating d
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Ancestral State Reconstruction Using BayesTraitstion process. Lacking fossil or other evidence about the past, ancestral states can be reconstructed. Three pieces of information are combined when reconstructing ancestral states: extant or known trait values (data); the evolutionary history, linking the species of interest (phylogeny); and the evo
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Reconstruction of State-Dependent Diversification: Integrating Phenotypic Traits into Molecular Phylmation have been developed to provide estimates of these processes. To that end, it is necessary to reconstruct molecular phylogenetic trees which summarize ancestor-descendant relationships as well as the timing of evolutionary events (i.e., rates). Nevertheless, diversification models show poor fi
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