Molecular and Genome Evolution

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 InstructorsInstructor's Resource Library (available to qualified adopters)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.

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

About the Author :
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.

Review :
"Importantly, this book goes beyond an overview of the current status of the field. By explaining the fundamental concepts of population genetics, which is essential to understanding molecular evolution, Graur gives his readers the necessary tools for a critical analysis of the different topics covered by his volume. Readers afraid of mathematical formulas should not be discouraged by the equations present throughout the book, as the mathematical concepts are clearly explained and illustrated. . . . This book is a must read for anyone lacking the molecular evolution background necessary to make sense of the current deluge of molecular data and, more generally, for anyone trying to keep up to date with the fast moving field of molecular and genome evolution." - Jean-Francois Gout, The Quarterly Review of Biology