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Cover

Molecular and Genome Evolution

Dan Graur

Publication Date - January 2016

ISBN: 9781605354699

612 pages
Hardcover
9 x 12 inches

In Stock

Retail Price to Students: $174.99

Describes the driving forces behind the evolutionary process at the molecular and genome levels

Description

This book describes the driving forces behind the evolutionary process at the molecular and genome levels, the effects of the various molecular mechanisms on the structure of genes, proteins, and genomes, the methodology and the analytical tools involved in dealing with molecular data from an evolutionary perspective, and the logic of evolutionary hypothesis testing. Evolutionary phenomena at the molecular level are detailed in a way that can be understood without much prerequisite knowledge of molecular biology, evolution, or mathematics. Numerous examples that support and clarify the theoretical arguments and methodological discussions are included.

For Instructors

Instructor's Resource Library
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This resource includes all figures (line-art illustrations and photographs) and tables from the textbook, provided as both high- and low-resolution JPEGs. All have been formatted and optimized for excellent projection quality. Also included are ready-to-use PowerPoint slides of all figures and tables.

About the Author(s)

Dan Graur is John and Rebecca Moores Professor in the Department of Biology and Biochemistry at the University of Houston and Professor Emeritus of Zoology at Tel Aviv University, Israel.

Table of Contents


    Introduction

    Chapter 1. The Molecular Basis of Biology and Evolution
    Nucleotide Sequences
    Genomes
    Genome constituents
    Somatic genome processing
    DNA Replication
    Transcription and Posttranscriptional Modifications of RNA
    Genes
    Protein-coding genes
    RNA-specifying genes
    Nontranscribed genes
    Pseudogenes
    Amino Acids
    Proteins
    Translation and Genetic Codes
    Information Flow among DNA, RNA, and Proteins
    Mutation
    Classification of mutations
    Point Mutations
    Segmental Mutations
    Recombination
    Deletions and insertions
    Inversions
    Spatial distribution of mutations
    Are Mutations Random?

    Chapter 2. Allele Dynamics in Populations
    Standing Genetic Variation
    Gene diversity
    Nucleotide diversity
    Structural variation
    What Is Evolution?
    Changes in Allele Frequencies
    Selection
    Codominance
    Dominance and recessiveness
    Overdominance and underdominance
    Random Genetic Drift
    Census Population Size and Effective Population Size
    Short-term effective population size
    Coalescence and long-term effective population size
    Factors conspiring to reduce the effective population size relative to the census population size
    Gene Substitution
    Fixation probability
    Fixation time
    Rate of gene substitution
    Mutational meltdown: The double jeopardy of small populations
    Nearly neutral mutations
    Second-Order Selection
    The evolution of mutation rates
    The evolution of mutational robustness
    Violations of Mendel's Laws of Inheritance
    Transmission Ratio Distortion
    Segregation distortion
    Postsegregation distortion
    Converting elements
    Sex allocation distortion
    Autonomous replicating elements
    Linkage Equilibrium and Disequilibrium
    Hitchhiking and Selective Sweep
    Molecular signatures of selective sweeps
    The evolution of lactase persistence in Africa and Europe
    Background Selection
    Epistasis
    The Driving Forces in Evolution
    The neo-Darwinian theory and the neutral mutation hypothesis
    The distribution of fitness effects
    A test of neutrality based on genetic polymorphism
    Consequences of Explosive Population Growth: Single-Nucleotide Variation in Humans

    Chapter 3. DNA and Amino Acid Sequence Evolution
    Nucleotide Substitution in a DNA Sequence
    Jukes and Cantor's one-parameter model
    Kimura's two-parameter model
    Number of Nucleotide Substitutions between Two DNA Sequences
    Number of substitutions between two noncoding sequences
    Substitution schemes with more than two parameters
    Violation of assumptions
    Saturation
    Number of Substitutions between Two Protein-Coding Genes
    Number of Amino Acid Replacements between Two Proteins
    Alignment of Nucleotide and Amino Acid Sequences
    Pairwise alignment
    Manual alignment
    The dot matrix method
    Scoring matrices and gap penalties
    Alignment algorithms
    Multiple-sequence alignment
    Quality of alignments
    Alignment of Genomic Sequences

    Chapter 4. Rates and Patterns of Molecular Evolution
    Rates of Point Mutation
    Rates of Segmental Mutations
    Rates of Nucleotide Substitution
    Rates of substitution in protein-coding sequences
    Rates of substitution in noncoding regions
    Causes of Variation in Substitution Rates
    The concept of functional constraint
    Quantifying the degree of protein tolerance toward amino acid replacements
    Synonymous versus nonsynonymous rates
    Variation among different gene regions
    Variation among genes
    Variables associated with protein evolutionary rates
    Evolutionary conservation and disease
    Relaxation of selection
    Selective intolerance toward indels
    Identifying positive and purifying selection
    Estimating the intensity of purifying selection
    Are slowly evolving regions always important?
    Male-Driven Evolution: Mutational Input and Slow-X Evolution
    Rates of Evolution under Positive Selection
    Prevalence of positive selection
    Fast-X evolution
    Rates of Evolution under Balancing Selection
    Patterns of Substitution and Replacement
    Patterns of spontaneous mutation
    Patterns of mutation and strand asymmetry
    Clustered multinucleotide substitutions: Positive selection or nonrandomness of mutation?
    Patterns of amino acid replacement
    What protein properties are conserved in protein evolution?
    Heterotachy
    Nonrandom Usage of Synonymous Codons
    Measures of codon usage bias
    Species-specific and universal patterns of codon usage
    Determinants of Codon Usage
    Interspecific variation in codon usage and amino acid usage
    Intragenomic variation in codon usage
    Translational efficiency and translation accuracy
    The tRNA adaptation index
    Intragenic variation in codon usage
    Indirect selection on codon usage
    Why do only some organisms have biased codon usages?
    Codon usage in unicellular and multicellular organisms
    Codon usage and population size
    Molecular Clocks
    Relative Rate Tests
    Local Clocks
    Nearly equal rates in mice and rats
    Lower rates in humans than in monkeys
    Higher rates in rodents than in other mammals
    Evaluation of the molecular clock hypothesis
    "Primitive" versus "advanced": A question of rates
    Causes of Variation in Substitution Rates among Evolutionary Lineages
    The DNA repair hypothesis
    The generation-time effect hypothesis
    The metabolic rate hypothesis
    The varying-selection hypothesis
    Are Living Fossils Molecular Fossils Too?
    Phyletic Gradualism, Punctuated Equilibria, and Episodic Molecular Evolution
    Rates of Substitution in Organelle DNA
    Mitochondrial rates of evolution
    Plastid rates of evolution
    Substitution and rearrangement rates
    Rates of Substitution in Viruses
    Human immunodeficiency viruses

    Chapter 5. Molecular Phylogenetics and Phylogenetic Trees
    Impacts of Molecular Data on Phylogenetic Studies
    Advantages of Molecular Data in Phylogenetic Studies
    Species and Speciation
    The species concept
    Speciation
    Terminology
    Phylogenetic Trees
    Rooted and unrooted trees
    Scaled and unscaled trees
    The Newick format
    Number of possible phylogenetic trees
    Tree balance
    True and inferred trees
    Gene trees and species trees
    Taxa and clades
    Types of Molecular Homology
    Types of Data
    Character data
    Assumptions about character evolution
    Polarity and taxonomic distribution of character states
    Distance data
    Methods of Tree Reconstruction
    Distance Matrix Methods
    Unweighted pair-group method with arithmetic means (UPGMA)
    Sattath and Tversky's neighbors-relation method
    Saitou and Nei's neighbor-joining method
    Maximum Parsimony Methods
    Weighted and unweighted parsimony
    Searching for the maximum parsimony tree
    Maximum Likelihood Methods
    Bayesian Phylogenetics
    Topological Comparisons
    Topological distance
    Consensus trees
    Supertrees
    Rooting Unrooted Trees
    Outgroup rooting
    Midpoint rooting
    Estimating Branch Lengths
    Calibrating Phylogenetic Trees and Estimating Divergence Times
    Assessing Tree Reliability
    The bootstrap
    Tests for two competing trees
    Problems Associated with Phylogenetic Reconstruction
    Strengths and weaknesses of different methods
    Minimizing error in phylogenetic analysis
    Genome Trees
    Genome trees based on shared gene content
    Genome trees from BLASTology
    Molecular Phylogenetic Examples
    Phylogeny of apes
    The utility of polarized character states: Cetartiodactyla and SINE phylogeny
    Molecular Phylogenetic Archeology
    The disextinction of the quagga
    The dusky seaside sparrow: A lesson in conservation biology
    Molecular Phylogenetics and the Law
    At the Limits of the Tree Metaphor: The Phylogeny of Eukaryotes and the Origin of Organelles
    The phylogeny of eukaryotes
    Origin of organelles
    Phylogenetic Trees as a Means to an End
    Parallelism and convergence as signifiers of positive selection
    Detecting amino acid sites under positive selection
    Reconstructing ancestral proteins and inferring paleoenvironments
    Mapping nonmolecular characters onto molecular trees

    Chapter 6. Reticulate Evolution and Phylogenetic Networks
    Networks
    Phylogenetic and Phylogenomic Networks
    The median network method
    The conditioned-reconstruction method
    Inferred reticulations: Are they real?
    Examples of Real-Life Phylogenetic Networks
    Reticulate evolution by recombination: A resurrected blood-group allele in humans
    Speciation by hybridization: The reticulate evolution of woodferns
    The Tree of Life Hypothesis
    The Vertical and Horizontal Components of Prokaryote Evolution
    Prokaryote taxonomy and the meaning of "species" in prokaryotes
    The Phylogeny of Everything
    The eukaryote-prokaryote divide and the taxonomic validity of Procaryota
    The Eubacteria-Archaebacteria divide
    The tripartite tree of life and its inadequacy
    The Origin of Eukaryotes
    The gradual origin hypothesis
    The fateful encounter hypothesis
    Eukaryotes as an "organizational upgrade"
    The nonrandom origin of operational and informational genes in eukaryotes
    Why genes in pieces? The origin of the nuclear membrane
    All complex life is eukaryotic: The energetics of gene expression
    The eukaryotic cell as a one-off innovation and a possible solution to the Fermi paradox
    Archaebacterial Systematics: Clade-Specific Archaebacterial Genes and Clade-Specific Horizontal Gene Imports from Eubacteria
    The Two Primary Domains of Life
    The Public Goods Hypothesis

    Chapter 7. Evolution by DNA Duplication
    Types of DNA Duplication
    Mechanisms of DNA Duplication
    Dating Duplications
    Gene Duplication and Gene Families
    The Prevalence of Gene Duplication
    Modes of Evolution of Multigene Families
    Divergent Evolution of Duplicated Genes
    Nonfunctionalization and gene loss
    Nonfunctionalization time
    Retention of original function following gene duplication
    Evolution of rRNA-specifying genes
    Neofunctionalization
    Multifunctionality and subfunctionalization
    Neosubfunctionalization
    Rates of Evolution in Duplicated Genes
    Rates and patterns of expression divergence between duplicated genes
    Human Globins
    Concerted Evolution
    Unequal crossing over
    Gene conversion
    Examples of gene conversion
    The relative roles of gene conversion and unequal crossing over
    Factors Affecting Concerted Evolution
    Number of repeats
    Arrangement of repeats
    Structure of the repeat unit
    Functional requirements and selection
    Population size
    Evolutionary Implications of Concerted Evolution
    Spread of advantageous mutations
    Retardation of paralogous gene divergence
    Generation of genic variation
    Methodological pitfalls due to concerted evolution
    Positive selection or biased gene conversion? The curious histories of HAR1 and FXY
    Birth-and-Death Evolution
    Expansion and contraction of gene families
    Examples of birth-and-death evolution
    The death of gene families
    Mixed Concerted Evolution and Birth-and-Death Evolution
    Polysomy
    Polyploidy
    Diploidization
    Distinguishing between gene duplication and genome duplication

    Chapter 8. Evolution by Molecular Tinkering
    Protein Domains
    Internal Gene Duplication
    Properties and prevalence of internal gene duplication
    Exon-Domain Correspondence
    Mosaic Proteins
    Exon Shuffling
    Phase limitations on exon shuffling
    Prevalence of domain shuffling and the evolutionary mobility of protein domains
    Domain shuffling and protein-protein interaction networks
    Gene Fusion and Fission
    Domain Accretion
    Strategies of Multidomain Gene Assembly
    Evolution by Exonization and Pseudoexonization
    Evolution of Overlapping Genes
    Alternative Splicing
    Sex determination and alternative splicing
    Evolution of alternative splicing
    Increasing proteome diversity: Alternative splicing or gene duplication?
    De Novo Origination of Genes
    Nested and Interleaved Genes
    Gene Loss and Unitary Pseudogenes: A Molecular Revisiting of the "Law of Use and Disuse"
    Functional Convergence
    Origin and Evolution of Spliceosomal Introns
    A Grand View of Molecular Tinkering: Suboptimality and Gratuitous Complexity
    Tinkering in action: The patchwork approach to the evolution of novel metabolic pathways
    Irremediable complexity by constructive neutral evolution

    Chapter 9. Mobile Elements in Evolution
    Mobile Elements, Transposable Elements, and Transposition
    Classification of Transposable Elements
    Conservative and replicative transposition
    DNA- and RNA-mediated transposition
    Enzymatic classification of transposable elements
    Autonomous and nonautonomous transposable elements
    Active and fossil transposable elements
    Taxonomic, developmental, and target-site specificity of transposition
    DNA-Mediated Transposable Elements
    Insertion sequences
    Transposons
    Nonautonomous DNA-mediated transposable elements
    Retroelements
    Retrons
    TERT genes
    Mitochondrial retroplasmids
    Group II introns and twintrons
    Retrotransposons
    Retroviruses
    Pararetroviruses
    Evolutionary origin of retroelements
    Nonautonomous and fossil retrotransposable elements
    LINEs and SINEs
    SINEs derived from 7SL RNA
    SINEs derived from tRNAs and SINEs containing 5S rRNA
    SINEs containing snRNA
    Mosaic SINEs
    Where there's a SINE, there's a LINE
    Rate of SINEs evolution
    Retrosequences
    Retrogenes
    Semiprocessed retrogenes
    Retropseudogenes
    Endogenous non-retroviral fossils
    The "Ecology" of Transposable Elements
    Transposable elements and the host genome: An evolutionary tug-of-war
    Transposable elements and segregation distortion
    Evolutionary dynamics of transposable-element copy number
    Genetic and Evolutionary Effects of Transposition
    Transposable elements as mutagens
    Transposable elements and somatic mosaicism
    The molecular domestication of transposable elements
    Transposition and Speciation
    Horizontal Gene Transfer
    Telltale signs of horizontal gene transfer
    Mechanisms of horizontal gene transfer among prokaryotes
    Prevalence and limitations of horizontal gene transfer in prokaryotes
    Genomic consequences of gene transfer among prokaryotes
    Clinical consequences of gene transfer among prokaryotes
    Horizontal Gene Transfer Involving Eukaryotes
    Horizontal gene transfer from eukaryotes to prokaryotes
    Horizontal gene transfer from prokaryotes to eukaryotes
    Horizontal transfer among eukaryotes
    Horizontal gene transfer among plants
    Horizontal transfer of a functional gene from fungi to aphids
    Horizontal transfer of transposable elements among animals
    Promiscuous DNA
    Transfer of intact functional genes to the nucleus
    Transfer of nonfunctional DNA segments from organelles to the nucleus: numts and nupts
    Rates and evolutionary impacts of norgDNA insertion

    Chapter 10. Prokaryotic Genome Evolution
    Genome Size in Prokaryotes
    The pangenome, the core genome, and the accessory genome
    Increases and decreases in prokaryotic genome sizes
    Genome Miniaturization
    Genome size reduction in intracellular symbionts and parasites
    The miniaturization of organelle genomes
    The evolution of mitochondrial genome sizes
    The evolution of plastid genome sizes
    The Minimal Genome
    The comparative genomics approach: Identifying the core genome of all life forms
    Probabilistic reconstruction of gene content in the last universal ancestor of life
    The experimental gene inactivation approach: Gene essentiality
    GC Content in Prokaryotes
    Possible explanations for variation in GC content
    Chargaff's parity rules
    GC Skew and Gene-Density Asymmetries Are Related to DNA Replication Biases
    Replichores and chirochores
    The location of genes in leading and lagging strands
    Chromosomal Evolution in Prokaryotes
    Evolution of chromosome number in prokaryotes
    Estimating the number of gene order rearrangement events
    Gene order evolution
    Operon evolution
    The Emergence of Alternative Genetic Codes

    Chapter 11. Eukaryotic Genome Evolution
    Functionality and nonfunctionality in eukaryotic genomes
    What is "function" in an evolutionary context?
    What do genomes do? An evolutionary classification of genomic function
    Changes in functional affiliation
    Detecting functionality at the genome level
    Phenotypic validation of positive selection
    What proportion of the human genome is functional?
    How much garbage DNA is in the human genome?
    Genome Size, DNA Content, and C Value
    Genome size variation and genomic content in eukaryotes
    Intraspecific variation in genome size
    Mutations That Increase or Decrease Genome Size
    The contribution of genome duplication to genome size
    The contribution of transposable elements to genome size
    Deletions and genome size
    Genomic Paradoxes in Eukaryotes
    The C-value paradox
    Possible solutions to the C-value paradox
    Why so much of the genome is transcribed--or is it?
    Life History and Cellular Correlates of Genome Size
    The nucleocytoplasmic ratio
    The coincidence hypothesis
    Nucleotypic hypotheses
    The nucleoskeletal hypothesis
    Is small genome size an adaptation to flight?
    The C-Value Paradox: The Neutralist Hypothesis
    Selfish DNA
    The mutational hazard hypothesis
    Is it junk DNA or is it indifferent DNA?
    Trends in Genome Size Evolution
    Is there an upper limit to genome size?
    Genome miniaturization in eukaryotes
    Protein-Coding Gene Number Variation and the G-Value Paradox
    Possible solutions to the G-value paradox
    The I value
    Gene Number Evolution
    Methodologies for Studying Gene Repertoire Evolution
    Gene-family cluster analysis
    Functional clustering of proteins
    Supervised machine learning and the subcellular localization of proteins
    Gene ontology
    Chromosome Number and Structure
    Chromosome number variation
    Chromosome morphology and chromosome types
    Chromosome size variation
    Euchromatin and heterochromatin
    Chromosomal Evolution
    Chromosome number evolution
    Chromosomal rearrangements
    Evolutionary patterns of chromosomal rearrangements
    Is gene order conserved?
    Gene Distribution Between and Within Chromosomes
    Gene density
    Do genes cluster by function?
    The Repetitive Structure of the Eukaryotic Genome
    Tandemly repeated sequences
    Mutational processes affecting repeat-unit number in tandemly repeated DNA
    The contribution of tandem repeats to genome size
    Do tandemly repeated DNA sequences have a function?
    Centromeres as examples of indifferent DNA
    Genome Compositional Architecture
    Segmentation algorithms and compositional domains
    Compositional architectures of mammalian nuclear genomes
    The origin and evolution of compositional domains

    Chapter 12. The Evolution of Gene Regulation, by Amy K. Sater
    Pretranscriptional Regulation
    Regulation by covalent modifications of histones
    DNA methylation
    Regulation at the Transcriptional Level
    Promoters
    Promoter evolution
    Divergent transcription
    Enhancers
    Shadow enhancers
    Insulators
    Posttranscriptional Regulation
    RNA interference
    Patterns of evolution of miRNAs
    Do miRNAs have a deep evolutionary history?
    Does translational regulation contribute to phenotypic evolution?

    Chapter 13. Experimental Molecular Evolution, by Tim F. Cooper
    What Is Experimental Evolution?
    The basic design of evolutionary experiments
    How to measure fitness and changes in fitness in evolutionary experiments
    The Contribution of Experimental Evolution to Evolutionary Biology
    Population divergence and the adaptive landscape metaphor
    Historical contingency
    Epistasis
    Mutation Dynamics
    Neutral mutation rates
    Non-neutral mutation rates
    Targets of Selection

    Literature Cited
    Index

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