Contents of "Introduction to Evolutionary Genomics"
Additions and Corrections are also shown here
### Contents of Printed Version ###
As of June 5th, A.S. 0014 (2014 A.D.)
Preface
Necessity of Evolutionary Studies
What is Evolution?
What is Genome?
Vitalism Versus Mechanism
Everything Is History
Genome as Republic of Genes
Structure of This Book
Acknowledgements
References
Part 1. Basic Processes of Genome Evolution
Chapter 1 Basic Metabolism Surrounding DNAs
1.1 Central Dogma of Molecular Biology
1.2 DNA Replication
1.2.1 Chemical Nature of DNA Molecules
1.2.2 DNA Replication Systems
1.3 Transcription
1.3.1 RNA
1.3.2 Messenger RNA (mRNA)
1.3.3 Transcription Machinery and Splicing
1.4 Translation and Genetic Codes
1.4.1 Transfer RNA (tRNA)
1.4.2 Genetic Codes
1.4.3 Ribosome and Translation
1.5 Proteins
1.5.1 Amino Acids
1.5.2 Four Strata of the Protein Structure
1.5.3 Protein Diversity
1.5.4 Protein Domains and Motifs
1.6 Genes
1.6.1 Protein Coding Genes
1.6.2 Chromosomes
References
Chapter 2 Mutation
2.1 Classification of mutations
2.1.1 What is mutation?
2.1.2 Temporal unit of mutation
2.1.3 Mutations affecting small regions of DNA sequences
2.1.4 Mutations affecting large regions of DNA sequences
2.2 Nucleotide substitution
2.2.1 Basic characteristics of nucleotide substitutions
2.2.2 Nucleotide substitutions in protein coding regions
2.2.3 Methylation creates "fifth" nucleotide
2.3 Insertion and deletion
2.3.1 Basic characteristics of insertion and deletion
2.3.2 Insertions and deletions of unique sequences
2.3.3 Insertions and deletions of repeat sequences
2.4 Recombination and gene conversion
2.4.1 Nature of gene conversion
2.4.2 Gene conversion on duplog pairs
2.5 Gene duplication
2.5.1 Classification of duplication events
2.5.2 Drift duplication
2.5.3 Genome duplication
2.6 Estimation of mutation rate
2.6.1 Direct and indirect methods
2.6.2 Direct method
2.6.3 Indirect method
2.6.4 Mutation rates of Bacteria, organella, and viruses
2.7 Mutations affecting phenotypes
2.7.1 What is phenotype?
2.7.2 Mutations in protein coding region
2.7.3 Mutations in non-coding region
References
Chapter 3 Phylogeny
3.1 DNA replications generate phylogenies
3.2 Genealogy of individuals
3.2.1 Genealogy of haploid individuals
3.2.2 Genealogy of diploid individuals
3.2.3 Paternal or maternal genealogy of diploid individuals
3.3 Gene genealogy
3.3.1 When a gene tree is identical to a genome tree
3.3.2 Gene phylogenies in diploids
3.3.3 Three layers of gene phylogenies
3.3.4 Orthology and paralogy
3.3.5 Gene conversions may twist the gene tree
3.3.6 Horizontal gene transfer and xenology
3.4 Species phylogeny
3.4.1 Two layers of species trees
3.4.2 Gene tree as the approximation of species tree
3.4.3 Gene tree may be different from species tree
3.5 Basic concepts of trees and networks
3.5.1 Mathematical definition
3.5.2 The number of possible tree topologies
3.5.3 How to describe trees and networks
Correction
Page 78, equation (3.7) should be as follows.
Tree_description = [(1, 2), (1, 3), (4, 5), (1, 4), (1, 6), (1, 7), (8, 9), (1, 8)]
Page 79, equation (3.10) should be as follows.
Tree_description = [(((((1, 2), 3), (4, 5)),6), 7), 8, 9]
3.5.4 Static networks and dynamic trees
3.5.5 Relationship between trees
3.6 Biological nature of trees and networks
3.6.1 Fission and fusion of species and populations
3.6.2 Importance of branch length
3.6.3 Trees and taxonomy
References
Chapter 4 Neutral Evolution
4.1 Neutral evolution as default process of the genome changes
4.1.1 Our world is finite
4.1.2 Unit of evolution
4.2 How to describe random nature of DNA propagation
4.2.1 Gene genealogy versus allele frequency change
4.2.2 Branching process
4.2.3 Coalescent process
4.2.4 Markov process
4.2.5 Diffusion process
4.2.6 A more realistic process of allele frequency change of selectively neutral situation
4.3 Expected evolutionary pattens under neutrality
4.3.1 Fixation probability
4.3.2 Rate of evolution
4.3.3 Amount of DNA variation kept in population
4.4 DNA polymorphism
4.4.1 Single nucleotide polymorphism (SNP)
4.4.2 Insertions and deletions (indel)
4.4.3 Repeat number polymorphism
4.4.4 Copy number variation
4.5 Mutation is the major player of evolution
4.6 Evolutionary rate under the neutral evolution
4.6.1 Molecular clock
4.6.2 Heterogeneous evolutionary rates among proteins
4.6.3 Heterogeneous evolutionary rates among protein parts
4.6.4 Heterogeneous evolutionary rates among organisms
4.6.5 Unit of evolutionary rate
4.7 Various features of neutral evolution
4.7.1 Synonymous and nonsynonymous substitutions
4.7.2 Junk DNA
4.7.3 Pseudogenes
4.7.4 Neutral evolution at macroscopic level
References
Chapter 5 Natural Selection
5.1 Basic concept of natural selection
5.2 Various types of positive selection
5.2.1 Balancing selection
5.2.2 Arms race between hosts and parasites
5.3 Natural selection on populations with large number of individuals
5.3.1 A series of simplifications in many theoretical models
5.3.2 The case for haploids
5.3.3 The case for diploids
5.3.4 Overdominant selection
5.4 Natural selection on populations with small number of individuals
5.4.1 Gene genealogy under natural selection
5.4.2 Diffusion approximation with natural selection
5.4.3 Fixation probability of a mutant
5.4.4 Slightly deleterious and nearly neutral mutations
5.4.5 Compensatory mutations
5.5 Natural selection at the genomic level
5.5.1 Selective sweep and background selection
5.5.2 Gain and loss of genes
5.5.3 Purifying selection at synonymous sites
5.5.4 Purifying selection at non-coding regions
5.5.5 Positive selection for ape and human genes
5.5.6 Detection of positive selection through genome-wide searches
References
Part 2 Evolving Genomes
Chapter 6 Brief History of Life
6.1 Origin of life
6.2 Evolution of the genetic code
6.3 Establishment of cell
6.4 Emergence of Eukaryotes
6.5 Multicellularization
6.6 From origin of vertebrates to emergence of modern human
References
Chapter 7 Prokaryote Genomes
7.1 Diversity of Prokaryotes and their genome sequencing efforts
7.2 The basic genome structure of Prokaryotes
7.3 GC content and oligonucleotide heterogeneity
7.4 Horizontal gene transfers
7.5 Codon usage
7.6 Metagenomes
References
Chapter 8 Eukaryote Genomes
8.1 Major differences between prokaryote and eukaryote genomes
8.2 Organella genomes
8.2.1 Mitochondria
8.2.2 Chroloplasts
8.2.3 Interaction between nuclear and organelle genomes
8.3 Intron
8.3.1 Classification of Intron
8.3.2 Introns early/late controversy
8.3.3 Functional regions in introns
8.4 Junk DNAs
8.4.1 Dispersed repeats
8.4.2 Tandem repeats
8.4.3 Pseudogenes
8.4.4 Junk RNAs and junk proteins
8.5 Evolution of eukaryote genomes
8.5.1 Genome duplication
8.5.2 RNA Editing
8.5.3 C value paradox
8.5.4 Conserved non-coding regions
8.5.5 Mutation rate and genome size
8.6 Genomes of multicellular organisms
8.6.1 Plant genomes
8.6.2 Fungi genomes
8.6.3 Animal genomes
8.6.3.1 Hox code
8.6.3.2 Genome of C. elegans
8.6.3.3 Insect genomes
8.6.3.4 Genomes of deuterostomes
8.7 Eukaryote viral genomes
References
Chapter 9 Vertebrate Genomes
9.1 Characteristics of vertebrate genomes
9.2 Two-round genome duplications
9.3 Features of protein coding genes
9.3.1 Genes shared with other taxonomic groups
9.3.2 Genes specific to vertebrates
9.3.3 Olfactory multigene families
9.3.4 Selective constraints in the protein coding sequences
9.4 Conserved noncoding regions
9.4.1 Evolutionary rates of noncoding sequences just upstream of protein coding regions
9.4.2 Highly conserved non-coding sequences
9.4.3 Conserved SINEs
9.4.4 Lineage-specific conserved noncoding sequences
9.5 Isochores
9.6 Genomes of specific vertebrate lineages
9.6.1 Teleost fish
9.6.2 Amphibians, birds, and reptiles
9.6.3 Mammals
9.6.3.1 Nonprimate mammals
9.6.3.2 Nonhuman primates
9.7 Ancient genomes
References
Chapter 10 Human Genomes
10.1 Overview of the human genome
10.2 Protein coding genes in the human genome
10.3 RNA coding genes and gene expression control regions in the human genome
10.4 Personal genomes
10.5 Genomic heterogeneity of the human genome
10.6 Genetic changes that made us human
10.7 Ancient human genomes
References
Part 3 Methods for Evolutionary Genomics
Chapter 11 Genome Sequencing
11.1 DNA extraction and purification
11.1.1 Special treatments for various samples
11.1.2 How to extract genomic DNA
11.2 Construction of genomic library
11.3 Determination of nucleotide sequence: chemical tactics
11.3.1 General overview
11.3.2 Sanger's method
11.3.3 Sequencing by synthesis
11.3.4 Physical distinguishing of each nucleotide
11.4 Determination of nucleotide sequences: computational tactics
11.4.1 Base call
11.4.2 Shotgun sequencing
11.4.3 Minimum tiling array
11.4.4 Haplotype sequence determination
11.4.5 Resequencing
References
Chapter 12 Omic Data Collection
12.1 Overview of omic worlds
12.2 Transcriptome
12.3 Proteome
12.4 Other omic data
References
Chapter 13 Databases
13.1 Overview of databases
13.2 Genome sequence databases
13.3 INSDC databases
13.4 Protein related databases
13.5 Literature databases
13.6 Other databases
References
Chapter 14 Sequence Homology Handling
14.1 What is homology?
14.2 Homology search
14.2.1 BLAST families
14.2.2 Examples of nucleotide sequence search using BLASTN
14.2.3 Examples of amino acid sequence search using BLAST families
14.2.4 Other homology search methods
14.2.5 Problem of homology search-dependent analyses
14.3 Pairwise alignment
14.3.1 Biologically true alignment
14.3.2 Mathematically optimum alignment
14.3.3 Methods using dynamic programming
14.3.4 Dot matrix method
14.4 Multiple alignment
14.4.1 Overview
14.4.2 CLUSTAL W
14.4.3 MAFFT
14.4.4 Example of amino acid sequence alignment
14.4.5 MISHIMA
14.4.6 Comparison of major multiple alignment softwares
14.5 Genomewide homology viewers
References
Chapter 15 Evolutionary Distances
15.1 Overview of evolutionary distance measures
15.2 Nucleotide substitution
15.2.1 Nucleotide difference and nucleotide substitution
15.2.2 Nucleotide substitution matrix
15.2.3 One-parameter method
15.2.4 Two-parameter method
15.2.5 Methods incorporating observed nucleotide frequencies
15.2.6 Other methods
15.2.7 Handling of heterogeneity among sites
15.3 Synonymous and nonsynonymous substitutions
15.3.1 Estimations of numbers of synonymous and nonsynonymous sites
15.3.2 Weightings for multiple paths
15.3.3 Correction of multiple hits
15.4 Amino acid substitution
15.4.1 Poisson correction
15.4.2 Dayhoff matrix and its descendants
15.3.2 Other methods
15.3.3 Numerical examples
15.5 Evolutionary distances not based on substitutions
References
Chapter 16 Tree and Network Building
16.1 Classification of tree-building methods
16.1.1 Classification by type of data
16.1.2 Classification by tree search algorithm
16.1.3 Character-state data
16.2 Distance matrix methods
16.2.1 UPGMA and WPGMA
16.2.2 Minimum deviation method and related methods
16.2.3 Minimum evolution method and related methods
Correction
Page 377, Table 16.3: A-G should be 1-7.
16.2.4 Transformed distance methods
16.2.5 Use of quartet OTUs for tree construction
Correction
Page 379, Table 16.4: A-G should be 1-7.
16.3 Neighbor-Joining method
16.3.1 What are neighbors?
16.3.2 Algorithm of the neighbor-joining method
16.3.3 A worked-out example of tree construction using the neighbor-joining method
16.3.4 Methods related to the neighbor-joining method
16.4 Phylogenetic network construction from distance matrix
16.5 Maximum parsimony method
16.5.1 The basic algorithm of the maximum parsimony method
16.5.2 Stepwise clustering algorithms for constructing maximum parsimony trees
16.5.3 Compatibility method
16.5.4 Theoretical problems of the maximum parsimony method
16.6 Maximum likelihood and Baysian methods
16.6.1 The principle of the maximum likelihood method
16.6.2 The basic algorithm of the maximum likelihood method
16.6.3 Stepwise clustering algorithm for the maximum likelihood method
16.6.4 Algorithm of the Baysian method
16.6.5 Theoretical problems of ML and Baysian methods
16.6 Phylogenetic network construction from character state data
16.7 Tree searching algorithms
16.8 Comparison of phylogenetic tree making methods
References
Chapter 17 Population Genomics
17.1 Evolutionary distances between populations
17.1.1 Distance between populations based on gene genealogy
17.1.2 Distance between species based on gene genealogy
17.1.3 Distance between populations based on allele frequency differences
17.1.4 Evolutionary distance between genomes
17.2 Mitochondrial DNA population genomics
17.2.1 Inference of gene genealogy
17.2.2 Population size fluctuation
17.2.3 Estimation of nucleotide substitution patterns
17.3 Population genomics of prokaryotes
17.4 Population genomics of nuclear genomes
17.4.1 Relationship of individuals and populations
17.4.2 Admixture
17.4.3 Introgression
17.4.4 Population size fluctuation
17.4.5 Genome wide association study
References
Index
Copyright (a) Naruya Saitou 2014