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James W. Brown
Principles of Microbial Diversity
Читать книгу Principles of Microbial Diversity - James W. Brown - Страница 1
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Страница 1
Table of Contents
List of Tables
List of Illustrations
Guide
Pages
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1
What Is Microbial Diversity?
Facets of microbial diversity
Morphological diversity
Structural diversity
Metabolic diversity
Ecological diversity
Behavioral diversity
Evolutionary diversity
The fundamental similarity of all living things
DNA
RNA
Protein
Function
Cells
Significance of the similarity between organisms
Questions for thought
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2
Context and Historical Baggage
The evolution of evolutionary thought
The chain of being
The evolutionary ladder
Early phylogenetic trees
Molecular phylogenetic trees
Taxonomy and phylogeny
Why is an understanding of phylogeny important?
The false eukaryote-prokaryote dichotomy
Questions for thought
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3
Phylogenetic Information
Deciding which organisms and sequences to use in the analysis
Features required of a good molecular clock
Clock-like behavior
The standard: small-subunit ribosomal RNA
Deciding which organisms to include
Obtaining the required sequence data
Databases
Obtaining sequences experimentally
Assembling sequences in a multiple-sequence alignment
Alignment based on conserved sequence
Alignment based on conserved structure
Questions for thought
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4
Constructing a Phylogenetic Tree
Tree construction: the neighbor-joining method
Generating a similarity matrix
Converting a similarity matrix into an evolutionary distance matrix
Generating a tree from a distance matrix
Rooting a tree with an outgroup
Molecular phylogenetic trees depict the relationships between gene sequences
How to read a phylogenetic tree
Scale
Terminal nodes
Internal nodes
Root
Branches
Tree representations
Example analysis
Interpretation
What good was this information?
Questions for thought
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5
Tree Construction Complexities
Substitution models
The special case of G
∙
C bias
Long-branch attraction
Treeing algorithms
Fitch-Margoliash: an alternative distance-matrix treeing method
Parsimony
Maximum likelihood
Bayesian inference
Bootstrapping
Questions for thought
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