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E-grāmata: Integrated Molecular Evolution

(Bowling Green State University, Ohio, USA)
  • Formāts: 594 pages
  • Izdošanas datums: 15-Sep-2016
  • Izdevniecība: CRC Press Inc
  • Valoda: eng
  • ISBN-13: 9781482230901
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  • Formāts: 594 pages
  • Izdošanas datums: 15-Sep-2016
  • Izdevniecība: CRC Press Inc
  • Valoda: eng
  • ISBN-13: 9781482230901
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"Molecular evolution, phylogenetics, genomics, and other related topics are all critical to understanding evolutionary processes. All too frequently, however, they are treated separately in textbooks and courses, such that students fail to connect all ofthe concepts, principles, and nuances of the evolutionary processes. Integrated Molecular Evolution brings these related areas together in one volume, facilitating student comprehension of often difficult concepts. Incorporating the emerging fields of genomics and bioinformatics with traditional fields such as evolution, genetics, and molecular biology, this volume explores a myriad of topics, including: Life on Earth and the possible origins of life; The evolution of organisms on Earth and the history of the study of evolution; Basic structures of DNA, RNA, proteins, and other biological molecules, and the synthesis of each; Molecular biology and the evolution, structure, and function of ribosomes; DNA replication and the various ways in which chromosomes are separated; Ways in which DNA can be changed to produce mutations, infectious causes of mutation, and repair of DNA; Definitions, evolution, and the importance of multigene families; Phylogenetic analysis and how researchers use the raw sequence data to reconstruct portions of evolutionary processes; Details of the genomes of a variety of organisms, from RNA viruses to eukaryotes, presented in order of complexity. Each chapter ends with a summary of key points, forming an effective review and enabling students to isolate critical material. The series of topics and the masterful integration of these topics lead students to a full understanding of evolution and the component processes that have led to biological evolution on Earth"--Provided by publisher.

The textbook is for students in a broad range of disciplines, and so assumes no specialized knowledge in any one field, but draws on such areas as evolution, geology, chemistry, biochemistry, molecular biology, genetics, taxonomy, bioinformatics, and of course molecular evolution itself. The second edition is about twice the size of the first, and covers life and evolution, biomolecules, genetics, multi-cellularity, molecular biology and bioinformatic methods, and genomes. Annotation ©2016 Ringgold, Inc., Portland, OR (protoview.com)

This book covers evolutionary studies using molecular data – sequences, structure, etc. – which are now routine and have become a central part of the life sciences curriculum. The new edition has been completely updated, responding to market needs by including more topics and increasing the depth of coverage for the topics included. This major revision nearly doubles the number of chapters. These changes establish this text as the leader in a large and growing pedagogical landscape.

Recenzijas

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

Preface xv
Acknowledgments xvii
Author xix
Section I Life and Evolution
Chapter 1 Definitions of Life
3(16)
Introduction
3(3)
RNA and Life
6(3)
Defining Life
9(4)
Imagining Cellular and Molecular Dimensions
13(3)
Key Points
16(1)
Additional Readings
16(3)
Chapter 2 Earth and Evolution
19(22)
Introduction
19(1)
What Is Evolution?
19(3)
Earth History
22(8)
A Short History of the Study of Evolution
30(5)
Earth History as One Year
35(2)
Key Points
37(1)
Additional Readings
38(3)
Section II Biomolecules
Chapter 3 DNA, RNA, and Proteins
41(16)
Introduction
41(1)
Nucleic Acids
42(9)
Translation
51(1)
Amino Acids and Polypeptides
52(2)
Lipids
54(1)
Carbohydrates
55(1)
Key Points
56(1)
Additional Readings
56(1)
Chapter 4 The Central Dogma and Beyond
57(14)
Introduction
57(1)
Ribosomal RNA
57(7)
Transfer RNA (tRNA)
64(1)
Messenger RNA
65(3)
Other Small Noncoding RNA
68(1)
Beyond the Central Dogma
69(1)
Key Points
69(1)
Additional Readings
69(2)
Chapter 5 Ribosomes and Ribosomal RNA
71(12)
Introduction
71(1)
Ribosomes as Ribozymes
71(1)
Origin of the Ribosome
72(2)
Translation
74(2)
How Many rDNA Copies Are Needed?
76(1)
Mechanisms for Increasing rRNA Gene Copy Number
77(3)
Complexity of Ribosomes
80(1)
Key Points
81(1)
Additional Readings
81(2)
Chapter 6 Structure of the Genetic Code
83(14)
Introduction
83(1)
Evolution of the Genetic Code
83(4)
Why a Triplet Codon?
87(3)
The First Genetic Code
90(2)
Life before Translation
92(3)
Key Points
95(1)
Additional Readings
96(1)
Chapter 7 DNA Replication
97(14)
Introduction
97(1)
Fidelity of Replication
97(4)
Variations of Replication
101(5)
Topology during Replication
106(1)
Replication of Chromosomes
107(1)
Key Points
108(1)
Additional Readings
109(2)
Chapter 8 DNA Segregation
111(20)
Introduction
111(1)
Variations on DNA Segregation in Bacteria and Archaea
111(2)
Mitosis
113(3)
Variations in Mitosis and the Cell Cycle
116(2)
Variations in Chromosome Number
118(2)
Changes in DNA Amount through the Cell Cycle
120(3)
Meiosis
123(2)
Sexual Reproduction
125(2)
Key Points
127(1)
Additional Readings
127(4)
Section III Genetics
Chapter 9 Mendelian and Non-Mendelian Characters
131(16)
Introduction
131(1)
Alleles
132(1)
The Basics of Mendelian Inheritance
132(5)
Codominance, Incomplete Dominance, Overdominance, and Underdominance
137(1)
Epistasis
138(2)
Quantitative Trait Loci
140(1)
Recombination and Linkage
141(1)
Non-Mendelian Traits
141(5)
Key Points
146(1)
Additional Readings
146(1)
Chapter 10 Population Genetics
147(12)
Introduction
147(1)
Hardy—Weinberg Equilibrium
148(2)
Population Size
150(1)
Life Histories
151(3)
Modes of Reproduction
154(4)
Key Points
158(1)
Additional Readings
158(1)
Chapter 11 Alleles through Time
159(14)
Introduction
159(1)
Natural Selection
160(2)
Levels of Selection
162(3)
Random Genetic Drift
165(1)
Mating and Dispersal
166(1)
Gene Flow
167(3)
Other Factors Affecting Allelic Proportions
170(1)
Key Points
170(1)
Additional Readings
171(2)
Chapter 12 Changes to DNA
173(14)
Introduction
173(1)
Classes of Mutations
173(1)
Causes of Mutations
174(5)
Mutation during Replication
179(1)
DNA Repair
180(2)
Genetic Recombination
182(3)
Key Points
185(1)
Additional Readings
185(2)
Chapter 13 Infectious Changes to DNA: Viruses, Plasmids, Transposons, and Introns
187(28)
Introduction
187(4)
Integration into Chromosomes
191(1)
Viruses
192(4)
Introns
196(8)
Transposable Elements
204(5)
Plasmids
209(1)
Key Points
210(1)
Additional Readings
211(4)
Section IV Multicellularity
Chapter 14 Multigene Families
215(14)
Introduction
215(2)
Ribosomal RNA Gene Family
217(1)
Globin Gene Family
218(4)
Bacterial Flagella Gene Family
222(1)
Laccase Gene Family
223(1)
Histone Gene Family
223(1)
Orthologs and Paralogs
224(1)
Polyploidization and Multigene Family Evolution
224(3)
Key Points
227(1)
Additional Readings
227(2)
Chapter 15 Horizontal Gene Transfer
229(18)
Introduction
229(2)
Plasm ids
231(3)
Viruses
234(1)
Symbionts and Organelles
235(4)
Parasites and Pathogens
239(3)
Origin of Gram-Negative Bacteria
242(1)
Signs of HGT
243(1)
Introns
244(2)
Key Points
246(1)
Additional Readings
246(1)
Chapter 16 Development: Part I—Cooperation among Cells
247(24)
Introduction
247(2)
Quorum Sensing
249(2)
Development in Animals
251(1)
Nematode Development
252(1)
Homeotic Genes and Proteins
253(8)
Arthropod Development
261(3)
Development in Vertebrates
264(2)
Hierarchy and Evolution of Homeotic Genes
266(2)
Key Points
268(1)
Additional Readings
269(2)
Chapter 17 Development: Part II—Plants
271(22)
Introduction
271(2)
Plant Morphology
273(1)
Development in Plants
274(3)
Gene Expression during Development
277(2)
Formation of Leaves and Floral Organs
279(8)
Plants versus Animals
287(4)
Key Points
291(1)
Additional Readings
292(1)
Chapter 18 Cancer
293(22)
Introduction
293(2)
Progression of Cancer
295(3)
Genes Involved in Cancer
298(3)
Types of Cancer
301(1)
Causes of Mutations in Carcinogenesis
301(10)
Point Mutations
302(1)
Recombination
302(3)
Amplification
305(1)
Viruses
306(3)
DNA Viruses
309(2)
Hormones
311(1)
Key Points
312(1)
Additional Readings
312(3)
Section V Molecular Biology and Bioinformatic Methods
Chapter 19 Extraction and Quantification of Biological Molecules
315(20)
Introduction
315(4)
Extraction of Nucleic Acids Using CTAB
319(2)
Purification of Organellar DNA
321(1)
Extraction of RNA
322(2)
Quantification of Nucleic Acids
324(1)
Agarose Gel Electrophoresis
324(5)
Extraction of Proteins
329(1)
Quantification of Proteins
330(1)
Polyacrylamide Gel Electrophoresis
331(1)
Key Points
332(1)
Additional Readings
333(2)
Chapter 20 Recombinant DNA and Characterization of Biological Molecules
335(22)
Introduction
335(1)
Polymerase Chain Reaction
335(3)
Recombinant DNA Methods
338(5)
Southern Hybridization
343(6)
Determination of Gene Copy Number
349(2)
Microscopy
351(2)
Protein Analysis
353(2)
Key Points
355(1)
Additional Readings
355(2)
Chapter 21 Sequencing and Alignment Methods
357(16)
Introduction
357(1)
Development of DNA Sequencing Methods
357(3)
High-Throughput Technologies
360(1)
Next-Generation Sequencing
361(4)
Protein Sequencing
365(2)
Sequence Homology Searches
367(1)
Aligning Sequences
368(2)
Key Points
370(1)
Additional Readings
371(2)
Chapter 22 Omics: Part I
373(10)
Introduction
373(1)
Genomics
373(3)
Transcriptomics
376(2)
Metagenomics/Metatranscriptomics
378(1)
Microbiomics
378(3)
Key Points
381(1)
Additional Readings
382(1)
Chapter 23 Omics: Part II
383(10)
Introduction
383(1)
Proteomics
383(3)
Structural Genomics
386(1)
RNAomics
387(1)
Epigenomics
388(1)
Metabolomics
389(1)
Functional Genomics
389(2)
Key Points
391(1)
Additional Readings
391(2)
Chapter 24 Species Concepts and Phylogenetics
393(26)
Introduction
393(1)
What Is a Species?
393(3)
Classification of Life
396(3)
Reconstruction of Evolutionary History
399(1)
Phylogenetics
400(1)
Tree Terminology
401(1)
Choosing a Genomic Region for Phylogentics
402(6)
Other Considerations When Performing Phylogenetic Analyses
408(1)
Models of Mutation
409(1)
Analyzing Aligned Sequences
410(1)
Unweighted Pair Group Method with Arithmetic Mean
410(1)
Neighbor Joining
410(1)
Maximum Parsimony
411(3)
Maximum Likelihood
414(1)
Bayesian Phylogenetic Analysis
415(1)
Bootstrapping
415(1)
Vertical versus Horizontal Evolutionary Events
416(1)
Key Points
417(1)
Additional Readings
417(2)
Chapter 25 Phylogenetic Networks and Reticulate Evolution
419(10)
Introduction
419(1)
Phylogenetic Analyses of Reticulate Events
420(1)
Advantages of Phylogenetic Networks
420(2)
Horizontal Gene Transfers
422(1)
Species Hybridization
423(1)
Recombination
424(1)
Transposition
425(1)
Reassortment
425(1)
Examples of Reticulate Evolution Events
426(1)
Key Points
427(1)
Additional Readings
428(1)
Chapter 26 Phylogenomics and Comparative Genomics
429(16)
Introduction
429(1)
Improvements in Sequencing and Phylogenomics
429(3)
What to Compare
432(1)
Single-Nucleotide Polymorphisms
433(1)
Microsatellites and Minisatellites
433(1)
How to Compare
434(1)
Testing for Selection
434(1)
Incongruent Trees
434(1)
Comparative Genomics
435(5)
Synteny
440(1)
Key Points
441(1)
Additional Readings
442(3)
Section VI Genomes
Chapter 27 RNA Viruses
445(16)
Introduction
445(3)
C-Value Paradox
448(1)
Genomes and Genomics
448(1)
RNA Virus Genomes
449(1)
Human Immunodeficiency Virus
449(4)
Influenza A Virus
453(4)
Ebola Virus
457(1)
Key Points
458(1)
Additional Readings
459(2)
Chapter 28 DNA Viruses
461(14)
Introduction
461(1)
Bacteriophage φX174
461(2)
Bacteriophage Lambda (X)
463(5)
Bacteriophage T4
468(3)
Mimivirus
471(3)
Key Points
474(1)
Additional Readings
474(1)
Chapter 29 Bacteria and Archaea
475(10)
Introduction
475(1)
Escherichia coli
475(2)
Photosynthetic Bacteria
477(2)
Aquifex
479(1)
Euryarchaeota
480(2)
Crenarchaeota
482(1)
Key Points
483(1)
Additional Readings
483(2)
Chapter 30 Mutualists and Pathogens
485(10)
Introduction
485(2)
Termite Gut Microbes
487(1)
Smallest Bacterial Genome
487(2)
Coresident Symbionts
489(1)
Animal Parasite
490(1)
Genome Mixing and Sorting
491(1)
Key Points
492(1)
Additional Readings
492(3)
Chapter 31 Endosymbionts and Organelles
495(20)
Introduction
495(1)
Intracellular Endosymbionts
495(1)
Mitochondria
496(7)
How Many Genes Make a Functional Mitochondrion?
503(3)
Chloroplasts
506(2)
How Many Genes Make a Functional Chloroplast?
508(2)
Differential Development and Function
510(1)
Chimeric Pathways
510(2)
Endosymbioses Leading to Other Organelles
512(2)
Key Points
514(1)
Additional Readings
514(1)
Chapter 32 Protein Trafficking
515(12)
Introduction
515(1)
Signal Peptides in Bacteria
515(3)
Signal Peptide Systems in Eukarya
518(2)
Protein Trafficking in Mitochondria
520(1)
Protein Trafficking in Chloroplasts
520(3)
Evolution of Protein Trafficking Systems
523(1)
Key Points
524(1)
Additional Readings
525(2)
Chapter 33 Eukaryotic Genomes
527(18)
Introduction
527(1)
Origin of the Nucleus and Mitochondrion
528(3)
Multicellularity
531(1)
Chromalveolata
531(1)
Opisthokonta
532(6)
Saccharomyces cerevisiae
532(2)
Caenorhabditis elegans
534(3)
Drosophila melanogaster
537(1)
Archaeplastida
538(5)
Arabidopsis thaliana
538(2)
Oryza sativa
540(3)
Key Points
543(1)
Additional Readings
544(1)
Chapter 34 Human Genome
545(12)
Introduction
545(1)
The Human Genome
545(3)
Medical Genetics
548(2)
Single-Nucleotide Polymorphisms
550(1)
Forensics
551(1)
Human Migration
551(3)
Key Points
554(1)
Additional Readings
554(3)
Index 557
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.