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Integrated Molecular Evolution, Second Edition

Edition:
2nd
Author(s):
Scott Orland Rogers
ISBN:
9781482230895
Format:
Hardback
Publication Date:
May 24, 2016
Content Details:
574 pages | 123 illustrations
Language:
English

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List Price:   $129.95

  
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  • About the Book

    Book Summary

    Evolutionary biology has increasingly relied upon tools developed in molecular biology that allow for the structure and function of macromolecules to be used as data for exploring the patterns and processes of evolutionary change. Integrated Molecular Evolution, Second Edition is a textbook intended to expansively and comprehensive review evolutionary studies now routinely using molecular data. This new edition has been thoroughly updated and expanded, and provides a basic summary of evolutionary biology as well as a review of current phylogenetics and phylogenomics.

    Reflecting a burgeoning pedagogical landscape, this new edition includes nearly double the number of chapters, including a new section on molecular and bioinformatic methods. Dedicated chapters were added on:

    • Evolution of the genetic code
    • Mendelian genetics and population genetics
    • Natural selection
    • Horizontal gene transfers
    • Animal development and plant development
    • Cancer
    • Extraction of biological molecules
    • Analytical methods
    • Sequencing methods and sequencing analyses
    • Omics
    • Phylogenetics and phylogenetic networks
    • Protein trafficking
    • Human genomics

    More than 400 illustrations appear in this edition, doubling the number included in the first edition, and over 100 of these diagrams are now in color.

    The second edition combines and integrates extensive summaries of genetics and evolutionary biology in a manner that is accessible for students at either the graduate or undergraduate level. It also provides both the basic foundations of molecular evolution, such as the structure and function of DNA, RNA and proteins, as well as more advanced chapters reviewing analytical techniques for obtaining sequences, and interpreting and archiving molecular and genomic data.

    Features

      • An integrated treatment of evolution, genetics, molecular biology and related topics.
      • Dramatic expansion and thorough re-imagining of the first edition – nearly doubling the number of chapters
      • Incorporates synthetic reviews of genomics and bioinformatics with traditional fields such as evolutionary biology, population genetics, and molecular structure and function
      • Thoroughly illustrated with over 400 figures—over 100 in color—detailing the essence of important principles and concepts

    Reviews

      Rogers (molecular biology and evolution, Bowling Green State Univ.) has created an engaging, readable, accessible introduction to the field of molecular evolution. The book is organized in sections that follow a logical progression. A brief discussion of life and the basic features of evolutionary theory is followed by sections on basic macromolecules and cellular processes, Mendelian and population genetics, gene families, means of gene transfer, the developmental processes in multicellular organisms, and methods of molecular analysis and omics. The work ends with chapters devoted to the genomes of various organisms and agents, from viruses through humans. In each chapter, the discussion is tied to how the topic affects or is affected by the process of evolution. Each chapter ends with a summary of key points and contains a list of additional sources. The illustrations are effective and enhance the text. The book will be most useful to readers with a basic knowledge of molecular biology and development, as the background topics are covered in an appropriately succinct fashion.

      --M. S. Kainz, Ripon College

      Summing Up: Highly recommended. Upper-division undergraduates through faculty. CHOICE

  • Contents

    LIFE AND EVOLUTION

    Definitions of Life
    Introduction
    RNA and Life
    Defining Life
    Imagining Cellular and Molecular Dimensions
    Key Points
    Additional Readings

    Earth and Evolution
    Introduction
    What Is Evolution?
    Earth History
    A Short History of the Study of Evolution
    Earth History as One Year
    Key Points
    Additional Readings

    BIOMOLECULES

    DNA, RNA, and Proteins
    Introduction
    Nucleic Acids
    Translation
    Amino Acids and Polypeptides
    Lipids
    Carbohydrates
    Key Points
    Additional Readings

    The Central Dogma and Beyond
    Introduction
    Ribosomal RNA
    Transfer RNA (tRNA)
    Messenger RNA
    Other Small Noncoding RNA
    Beyond the Central Dogma
    Key Points
    Additional Readings

    Ribosomes and Ribosomal RNA
    Introduction
    Ribosomes as Ribozymes
    Origin of the Ribosome
    Translation
    How Many rDNA Copies Are Needed?
    Mechanisms for Increasing rRNA Gene Copy Number
    Complexity of Ribosomes
    Key Points
    Additional Readings

    Structure of the Genetic Code
    Introduction
    Evolution of the Genetic Code
    Why a Triplet Codon?
    The First Genetic Code
    Life Before Translation
    Key Points
    Additional Readings

    DNA Replication
    Introduction
    Fidelity of Replication
    Variations of Replication
    Topology During Replication
    Replication of Chromosomes
    Key Points
    Additional Readings

    DNA Segregation
    Introduction
    Variations on DNA Segregation in Bacteria and Archaea
    Mitosis
    Variations in Mitosis and the Cell Cycle
    Variations in Chromosome Number
    Changes in DNA Amount through the Cell Cycle
    Meiosis
    Sexual Reproduction
    Key Points
    Additional Readings

    GENETICS

    Mendelian and Non-Mendelian Characters
    Introduction
    Alleles
    The Basics of Mendelian Inheritance
    Codominance, Incomplete Dominance, Overdominance, and Underdominance
    Epistasis
    Quantitative Trait Loci
    Recombination and Linkage
    Non-Mendelian Traits
    Key Points
    Additional Readings

    Population Genetics
    Introduction
    Hardy–Weinberg Equilibrium
    Population Size
    Life Histories
    Modes of Reproduction
    Key Points
    Additional Readings

    Alleles through Time
    Introduction
    Natural Selection
    Levels of Selection
    Random Genetic Drift
    Mating and Dispersal
    Gene Flow
    Other Factors Affecting Allelic Proportions
    Key Points
    Additional Readings

    Changes to DNA
    Introduction
    Classes of Mutations
    Causes of Mutations
    Mutation During Replication
    DNA Repair
    Genetic Recombination
    Key Points
    Additional Readings

    Infectious Changes to DNA: Viruses, Plasmids, Transposons, and Introns
    Introduction
    Integration Into Chromosomes
    Viruses
    Introns
    Transposable Elements
    Plasmids
    Key Points
    Additional Readings

    MULTICELLULARITY

    Multigene Families
    Introduction
    Ribosomal RNA Gene Family
    Globin Gene Family
    Bacterial Flagella Gene Family
    Laccase Gene Family
    Orthologs and Paralogs
    Polyploidization and Multigene Family Evolution
    Key Points
    Additional Readings

    Horizontal Gene Transfer
    Introduction
    Plasmids
    Viruses
    Symbionts and Organelles
    Parasites and Pathogens
    Origin of Gram Negative Bacteria
    Signs of HGT
    Introns
    Key Points
    Additional Readings

    Development: Part I—Cooperation among Cells
    Introduction
    Quorum Sensing
    Development in Animals
    Nematode Development
    Homeotic Genes and Proteins
    Arthropod Development
    Development in Vertebrates
    Hierarchy and Evolution of Homeotic Genes
    Key Points
    Additional Readings

    Development: Part II—Plants
    Introduction
    Plant Morphology
    Development in Plants
    Gene Expression during Development
    Formation of Leaves and Floral Organs
    Plants versus Animals
    Key Points
    Additional Readings

    Cancer
    Introduction
    Progression of Cancer
    Genes Involved in Cancer
    Types of Cancer
    Causes of Mutations in Carcinogenesis
    Hormones
    Key Points
    Additional Readings

    MOLECULAR BIOLOGY AND BIOINFORMATIC METHODS

    Extraction and Quantification of Biological Molecules
    Introduction
    Extraction of Nucleic Acids Using CTAB
    Purification of Organellar DNA
    Extraction of RNA
    Quantification of Nucleic Acids
    Agarose Gel Electrophoresis
    Extraction of Proteins
    Quantification of Proteins
    Polyacrylamide Gel Electrophoresis
    Key Points
    Additional Readings

    Recombinant DNA and Characterization of Biological Molecules
    Introduction
    Polymerase Chain Reaction
    Recombinant DNA Methods
    Southern Hybridization
    Determination of Gene Copy Number
    Microscopy
    Protein Analysis
    Key Points
    Additional Readings

    Sequencing and Alignment Methods
    Introduction
    Development of DNA Sequencing Methods
    High-Throughput Technologies
    Next-Generation Sequencing
    Protein Sequencing
    Sequence Homology Searches
    Aligning Sequences
    Key Points
    Additional Readings

    OMICS: Part I
    Introduction
    Genomics
    Transcriptomics
    Metagenomics/Metatranscriptomics
    Microbiomics
    Key Points
    Additional Readings

    OMICS: Part II
    Introduction
    Proteomics
    Structural Genomics
    RNAomics
    Epigenomics
    Metabolomics
    Functional Genomics
    Key Points
    Additional Readings

    Species Concepts and Phylogenetics
    Introduction
    What Is a Species?
    Classification of Life
    Reconstruction of Evolutionary History
    Phylogenetics
    Tree Terminology
    Choosing a Genomic Region for Phylogenetics
    Other Considerations When Performing Phylogenetic Analyses
    Models of Mutation
    Analyzing Aligned Sequences
    Unweighted Pair Group Method with Arithmetic Mean
    Neighbor Joining
    Maximum Parsimony
    Maximum Likelihood
    Bayesian Phylogenetic Analysis
    Bootstrapping
    Vertical versus Horizontal Evolutionary Events
    Key Points
    Additional Readings

    Phylogenetic Networks and Reticulate Evolution
    Introduction
    Phylogenetic Analyses of Reticulate Events
    Advantages of Phylogenetic Networks
    Horizontal Gene Transfers
    Species Hybridization
    Recombination
    Transposition
    Reassortment
    Examples of Reticulate Evolution Events
    Key Points
    Additional Readings

    Phylogenomics and Comparative Genomics
    Introduction
    Improvements in Sequencing and Phylogenomics
    What to Compare
    Single-Nucleotide Polymorphisms
    Microsatellites and Minisatellites
    How to Compare
    Testing for Selection
    Incongruent Trees
    Comparative Genomics
    Synteny
    Key Points
    Additional Readings

    GENOMES

    RNA Viruses
    Introduction
    C-Value Paradox
    Genomes and Genomics
    RNA Virus Genomes
    Human Immunodeficiency Virus
    Influenza A Virus
    Ebola Virus
    Key Points
    Additional Readings

    DNA Viruses
    Introduction
    Bacteriophage ΦX174
    Bacteriophage Lambda (λ)
    Bacteriophage T4
    Mimivirus
    Key Points
    Additional Readings

    Bacteria and Archaea
    Introduction
    Escherichia coli
    Photosynthetic Bacteria
    Aquifex
    Euryarchaeota
    Crenarchaeota
    Key Points
    Additional Readings

    Mutualists and Pathogens
    Introduction
    Termite Gut Microbes
    Smallest Bacterial Genome
    Coresident Symbionts
    Animal Parasite
    Genome Mixing and Sorting
    Key Points
    Additional Readings

    Endosymbionts and Organelles
    Introduction
    Intracellular Endosymbionts
    Mitochondria
    How Many Genes Make a Functional Mitochondrion?
    Chloroplasts
    How Many Genes Make a Functional Chloroplast?
    Differential Development and Function
    Chimeric Pathways
    Endosymbioses Leading to Other Organelles
    Key Points
    Additional Readings

    Protein Trafficking
    Introduction
    Signal Peptides in Bacteria
    Signal Peptide Systems in Eukarya
    Protein Trafficking in Mitochondria
    Protein Trafficking in Chloroplasts
    Evolution of Protein Trafficking Systems
    Key Points
    Additional Readings

    Eukaryotic Genomes
    Introduction
    Origin of the Nucleus and Mitochondrion
    Multicellularity
    Chromalveolata
    Opisthokonta
    Archaeplastida
    Key Points
    Additional Reading

    Human Genome
    Introduction
    The Human Genome
    Medical Genetics
    Single Nucleotide Polymorphisms
    Forensics
    Human Migration
    Key Points
    Additional Readings