Integrated Molecular Evolution: 2nd Edition (Hardback) book cover

Integrated Molecular Evolution

2nd Edition

By Scott Orland Rogers

CRC Press

574 pages | 123 Color Illus. | 291 B/W Illus.

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pub: 2016-05-24
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Description

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.

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

Table of 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

About the Author

Scott Orland Rogers is a professor of molecular biology and evolution at Bowling Green State University, Bowling Green, Ohio. He received his PhD in plant molecular biology from the University of Washington, Seattle. He was an assistant professor and associate professor at the State University of New York College of Environmental Science and Forestry before moving to BGSU. He has taught courses in biology, botany, cell physiology, molecular biology, molecular genetics, bioinformatics, and molecular evolution. Research in his lab includes studies of microbes and nucleic acids preserved in ice, life in extreme environments, group I introns, molecular microbial phylogenetics, microbial metagenomics/metatranscriptomics, ancient DNA, and plant development.

Subject Categories

BISAC Subject Codes/Headings:
SCI017000
SCIENCE / Life Sciences / Cytology
SCI027000
SCIENCE / Life Sciences / Evolution
SCI049000
SCIENCE / Life Sciences / Biology / Molecular Biology