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GENETICS
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ANALYSIS OF GENES AND

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GENOMES
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Daniel L. Hartl, PhD NOT FOR SALE OR DISTRIBUTION
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Bruce J. Cochrane, PhD

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Brief Contents iii
Brief Contents
Unit I Defining and Working

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Learning, LLC 1
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2 DNA Structure and Genetic Variation 40
Unit II Transmission Genetics 81

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4 The Chromosomal Basis of Inheritance 120
5 Genetic Linkage and Chromosome Mapping 159
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Karyotypes ©Behavior
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7 The Genetic Basis of Complex Traits 245
8 Genetics of Bacteria and Their Viruses 279
Unit III Organization

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10 DNA Replication and Sequencing 353
11 Mutation, Repair, and Recombination 382
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12 Molecular Biology of Gene Expression 424
13 Molecular Mechanisms of Gene Regulation 466
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15 Genetic Control of Development 568
16 Molecular Genetics of the Cell Cycle and Cancer 609
Unit V Variation
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iv Contents
Contents
Preface xv © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LL
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What’s New in the Ninth Edition xxii
Teaching Tools xxvi
Acknowledgments xxviii
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Unit I Defining and Working with GENES 1
1 Genes,
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Genomes, © Jones & Bartlett Learning, LLC 2
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Objectives & Science NOT FOR1.5
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Expression: The Central
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1.1 DNA as the Genetic Material 4 Transcription 24
Experimental Proof of the Genetic Translation 25
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1.2 DNA Structure and Replication 8 Variation in Populations 29
An Overview of DNA Replication 10 1.7 Genes and Environment 30
1.3 Genes and Proteins 11 1.8 The Molecular Unity of Life 31
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Genomes and Proteomes 32
1.4 Genetic Analysis 15
ROOTS OF DISCOVERY: The Black Urine
Mutant Genes and Defective Proteins 16 Disease 14
Complementation Test for Mutations in the ROOTS OF DISCOVERY: One Gene,
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2 DNA Structure and Genetic Variation 40

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2.1 Genetic Differences Among 2.4 The Separation and Identification of
Individuals 41 Genomic DNA Fragments 51
DNA Markers as Landmarks Restriction Enzymes and Site-Specific
in Chromosomes 41 DNA Cleavage 52
2.2 T
he Terminology of
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Analysis 43
Nucleic Acid Hybridization 56
2.3 The Molecular Structure of DNA 44
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The Double Helix 46 Constraints on DNA Replication: Primers
Base Pairing
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Contents v
The Polymerase Chain Reaction 60 © Jones &2.7Bartlett

Applications of DNALLC
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2.6 Types of DNA Markers Present in Genetic Markers,
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Restriction Fragment Length Other Uses for DNA Markers 71
Polymorphisms 64 ROOTS OF DISCOVERY: The Double
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Tandem Repeat Polymorphisms 67
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Copy-Number Variation 70 Genotyping 68
Unit II Transmission Genetics 81
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Principles of Segregation
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Learning Objectives & Science Molecular Markers in Human
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Epistasis 105
Verification of Segregation 91
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The Testcross and the Backcross 92
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Learning Objectives
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vi Contents
4.5 Probability in the Prediction The Chi-Square

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of Progeny Distributions 144
Are Mendel’s Data Too Good to Be
Using the Binomial Distribution
True? 150
in Genetics 145
Meaning of the Binomial Coefficient 146 ROOTS OF DISCOVERY: Grasshopper,
Grasshopper 134
4.6 Testing Goodness
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Random Variables and Distributions 147 Male 138
5 Genetic Linkage and Chromosome Mapping 159

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5.1 Linkage and Recombination of Genes Three-Point Testcross 176
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Each Pair of Linked Genes Has a
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Recombination 164 Unordered Tetrads 180
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X Chromosome 209 Deletions 217

Contents vii
Deletion Mapping 218 Pseudolinkage

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Duplications 219 Robertsonian Translocations
Unequal Crossing Over in Human and Trisomy 21 230
Red–Green Color Blindness 220 Translocation Complexes in
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Reciprocal Risks of Autism and 6.6 Genomic Position Effects on Gene
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ROOTS OF DISCOVERY: Lyonization
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7 The Genetic Basis of Complex Traits 245
Learning Objectives & Science 7.4 Correlation Between Relatives 259
Competencies 246 Covariance and Correlation 259
7.1 Complex Traits
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The Graphical Meaning
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Continuous Traits 249 Long-Term Artificial Selection 264 LLC
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Genetics and Environment 7.7 Identification of Genes Affecting
Combined 254 Complex Traits 267
Genotype-by-Environment Interaction and Linkage Analysis in the Genetic Mapping
Association 255
of Quantitative-Trait Loci 267
7.3 Heritability 256 Genome-Wide Association Studies 268
The Number of Genes Affecting Candidate Genes for Complex Traits 269
Complex Traits 257 ROOTS OF DISCOVERY: A Maize’n Grass 251
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8 Genetics of Bacteria and Their Viruses 279

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Mutant Phenotypes 282
8.1 Plasmids and Genetic Exchange 280 Isolating Auxotrophs 283
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Plasmid 281
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viii Contents
8.4 Genetic Exchange and Conjugation 286 Fine Structure

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9 Molecular Organization of Chromosomes and Genomes 320

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The Nucleosome Core Particle 328 of the Centromere 341
Chromosome Territories in the 9.8 Molecular Structure of the Telomere 343
Nucleus 331 Telomere Length Limits the Number
Chromosome Condensation 332 of Cell Doublings 346
Polytene Chromosomes 333 ROOTS OF DISCOVERY: Telomeres:
© Jones & Bartlett Learning, LLC The Beginning of the © End
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10 DNA Replication and Sequencing 353
Learning Objectives & Science 10.3 Initiation of DNA Replication 361
Competencies 354 Unwinding, Stabilization, and Stress
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Elongation, © Jones361
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Double-Stranded DNA 355 10.4 The Elongation Process
The Meselson–Stahl Experiment 355 and Proofreading 363
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Rolling-Circle Replication 360 The Joining of Precursor Fragments 366

Contents ix
10.5 Terminating Replication 367 © Jones &10.7 Exploiting

Bartlett the System:
Learning, LLCDNA
10.6 Replication in Eukaryotes 367 Sequencing 372
Semiconservative Replication of DNA Sanger Sequencing 373
in Chromosomes 368 Next-Generation Sequencing 374
Multiple Origins and Bidirectional ROOTS OF DISCOVERY: Replication
Replication in Eukaryotes 368 by Halves 358
Initiation 370
Termination and the Problem
of Telomeres 372
11 Mutation, Repair, and Recombination 382

Learning Objectives & Science Chemical Agents That Modify DNA 399
NOT FOR SALE383
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Ultraviolet Irradiation 400
11.1 Types of Mutations 383 Ionizing Radiation 401
Germ-Line and Somatic Genetic Effects of the Chernobyl
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Classification by Function 384 NOT FOR11.6 Mechanisms of
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11.2 The Molecular Basis of Mutation 385 Mismatch Repair 405
Nucleotide Substitutions 385 Base-Excision Repair 407
Missense Mutations: The Example AP Repair 408 ©
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Test for Mutagen/Carcinogen
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Unit IV Gene Expression 423

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x Contents
12.5 Transcription in Eukaryotes 433 InitiationLearning,

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RNA Polymerases 433 Elongation 445
Promoters and Promoter Recognition 434 Release 447
Initiation 435 Translational Proofreading and Premature
Elongation 435 Termination 448
Termination © Jones
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5 Capping and 3 Polyadenylation 437 12.9 The Standard Genetic Code 454
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Sequences 437
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Characteristics of
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© Jones & BartlettEffects of Intron
Learning, LLCMutations 441 © Jones & Bartlett
Nonsense Learning, LLC458
Suppression
Exon Shuffling
NOT FOR SALE OR DISTRIBUTION in the Origin NOT FORROOTS
SALE OF ORDISCOVERY:
DISTRIBUTIONMessenger
of New Genes 442 “Light” 432
12.7 Protein Synthesis 443 ROOTS OF DISCOVERY: Poly-U 453
Initiation in Prokaryotes 443
13 MolecularNOT
Mechanisms of DISTRIBUTION
FOR SALE OR Gene Regulation NOT FOR SALE 466
OR DISTRIBUT
Learning Objectives & Science 13.5 Transcriptional Regulation in
Competencies 467 Eukaryotes 484
13.1 Transcriptional Regulation in Galactose Metabolism in Yeast 484
Prokaryotes 467 Transcriptional Activator Proteins 486
Inducible and Repressible Systems Transcriptional Enhancers
NOT of FOR SALE
Negative OR DISTRIBUTION
Regulation 468 NOT FOR SALE OR DISTRIBUTION
and Transcriptional Silencers 488
Positive Regulation 469 Deletion Scanning 488
Stochastic Noise in Gene Expression 469 The Eukaryotic Transcription
13.2 The Operon System Complex 489
© Jones & BartlettofLearning, LLC
Gene Regulation 470 © Jones & Bartlett Learning, LLC
Chromatin-Remodeling
Lac Mutants 470
2 NOT FOR SALE OR
Complexes DISTRIBUTION
491
Inducible and Constitutive Synthesis Alternative Promoters 493
and Repression 470 13.6 Epigenetic Mechanisms of
Repressors, Operators, and Transcriptional Regulation 497
Promoters© 471
Jones & Bartlett Learning, LLC © Jones
Cytosine Methylation 497 & Bartlett Learning, LL
The Operon NOT FORofSALE
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Transcriptional
Regulation 472 Inactivation 497
Stochastic Noise in Lac Expression 473 Genomic Imprinting in the Female
Positive Regulation of the Lactose and Male Germ Lines 498
Operon 473
© Jones & Bartlett Learning, LLC 13.7©Regulation
Jones & Through
BartlettRNA
Learning, LLC
Processing
NOT Regulation
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ORTryptophan Operon 475
DISTRIBUTION and Decay
NOT FOR SALE499 OR DISTRIBUTION
13.3 Regulation Through Transcription Alternative Splicing 499
Termination 478 Messenger RNA Stability 499
Attenuation 478 13.8 Noncoding RNAs
Riboswitches
© Jones & Bartlett Learning, LLC 481 and Regulation
© Jones & Bartlett Learning,500LLC
NOT FOR SALE13.4
OR Regulation in Bacteriophage
DISTRIBUTION NOT FOR SALEInterfering RNAs 500
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Lambda 481 Long Noncoding RNA 504

Contents xi
13.9 Translational Control 505 Mating-Type

© Jones & Bartlett Interconversion
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Regulatory
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Translation 506 Type 511
13.10 Programmed DNA ROOTS OF DISCOVERY: Operator?
Rearrangements 507 Operator? 476
Gene Amplification 507
© Jones & Bartlett Learning, LLC ROOTS OF DISCOVERY: Double Trouble 502
Antibody and T-Cell Receptor
Variability 507
14 Manipulating Genes and Genomes 519

© Learning
Jones &Objectives
Bartlett&Learning,
Science LLC 14.5©
Functional
Jones &Genomics 538
Bartlett Learning, LLC
Competencies 520 Chromatin Immunoprecipitation 543
14.1 Site-Specific DNA Cleavage and Two-Hybrid Analysis of Protein–Protein
Cloning Vectors 521
Interactions 544
Production of DNA Fragments
14.6 Transgenic Organisms 547
with Defined Ends 521
© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning,
Germ-Line LLC in Animals 547
Transformation
Recombinant DNA Molecules 522
NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OREngineering
Genetic DISTRIBUTION
in Plants 551
Plasmid, Lambda, and Cosmid
Vectors 522 Transformation Rescue 552
14.2 Cloning Strategies 524 Site-Directed Mutagenesis
Joining DNA Fragments 524 and Knockout Mutations 553
Insertion of a Particular DNA Molecule into Gene Expression “Knockdown”
a Vector 526 with RNAi 554
The Use of Reverse Transcriptase: cDNA 14.7 Gene Editing 555
and RT-PCR 526
CRISPR–Cas9 in Practice 555
14.3 Detection of Recombinant
© Jones & Bartlett 14.8©Some Applications of Learning,
Genetic
Molecules 528Learning,
LLC Jones & Bartlett LLC
NOT Gene
FORInactivation
SALE ORinDISTRIBUTION Engineering 559
the Vector
Molecule 528 Giant Salmon with Engineered
Growth Hormone 559
Screening for Particular
Recombinants 530 Nutritionally Engineered Rice 559
© Jones & Bartlett
14.4 GLearning, LLC
enomics 531 © Jones & Bartlett Learning,
Production of UsefulLLC
Proteins 560
Genomic Sequencing 531 NOT FOR SALE OR DISTRIBUTION
Genetic Engineering with Animal
Sequencing the Human Viruses 560
Genome 532 ROOTS OF DISCOVERY: Hello, Dolly! 548
Genome Annotation 533 THE CUTTING EDGE: Editing
© Jones
Comparative & Bartlett
Genomics 535 Learning, LLC the Muscular Dystrophy
© Jones
Gene& 557
Bartlett Learning, LL
15 Genetic Control of Development 568
Learning Objectives & Science Early Development and Activation of the
Competencies 569 Zygotic Genome 573
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Determinants of LLC © Jones & Bartlett Learning, LLC
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Animals 570
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Autonomous Development
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Intercellular Signaling 570 Programmed
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Loss-of-Function and Gain-of-Function
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xii Contents
Epistasis in the Analysis of Developmental Homeotic Genes 592

Switches 579 Master Control Genes in Evolution 593
15.4 Genetic Control of Development in 15.5 Regulatory RNAs in Development 595
Drosophila 582
Micro RNA–Based Regulation
Maternal-Effect Genes and Zygotic in C. elegans 595
Genes 584
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15.6 Genetic Control of Development in
Coordinate Genes 586
Higher Plants 598
Gap Genes 589
Flower Development in Arabidopsis 599
Pair-Rule Genes 589
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Segment-Polarity Genes 590LLC © Jones & Bartlett
Organs 600
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ROOTS OF DISCOVERY: Distinguished
Hierarchy 590 Lineages 575
Metamorphosis of the Adult Fly 592 ROOTS OF DISCOVERY: Embryogenesis 588
© Jones &16
Bartlett Learning,
Molecular LLC
Genetics of the Cell © Jonesand
Cycle & Bartlett
Cancer Learning, LLC 609
Learning Objectives & Science The Centrosome Duplication
Competencies 610 Checkpoint 625
16.1 The Cell Cycle 610 The Spindle Assembly Checkpoint 625
Key Events in the Cell Cycle 610 Consequences of Checkpoint Failure 625
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LLC © Jones & Bartlett Learning, LL
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Cycle 612 NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUT
Oncogenes and Proto-oncogenes 627
16.2 Genetic Analysis of the Cell Cycle 613 Tumor-Suppressor Genes 628
Mutations Affecting Progression 16.6 Hereditary Cancer Syndromes 631
Through the Cell Cycle 613
Defects in DNA Repair 634
© Jones & Bartlett
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Through LLC
the Cell © Jones & Bartlett Learning, LLC
16.7 Genetics of the Acute Leukemias 636
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16.8 The Genomics and Transcriptomics of
Cyclins and Cyclin-Dependent
Cancer 637
Protein Kinases 615
Pancreatic Cancer: The Mutational
Targets of the Cyclin–CDK
Landscape 638
© Jones & BartlettComplexes
Learning,618LLC © Jones & Bartlett Learning,
Pancreatic LLC
Cancer: The Transcriptiosomal
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Transitions 618
From Genes and Transcripts to
Protein Degradation Helps Regulate
Therapy? 641
the Cell Cycle 620
ROOTS OF DISCOVERY: Cycle-Ops 617
16.4 Checkpoints in the Cell Cycle 621
© Jones & Bartlett Learning, LLC ROOTS OF DISCOVERY: © Jones & Bartlett Learning, LL
Two Hits,
The DNA Damage Checkpoint 622
NOT FOR SALE OR DISTRIBUTIONTwo Errors 635 NOT FOR SALE OR DISTRIBUT
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17© Mitochondrial DNA and Extranuclear Inheritance

650
Learning Objectives & Science 17.2 Patterns of Extranuclear
Competencies 651 Inheritance 655
17.1 Origin and Molecular Genetics of Maternal Inheritance of Animal
Organelles 651 Mitochondria 655
Organelle Genomes 652 Maternal Inheritance and Maternal
© Jones & BartlettRNA
Learning, LLC
Editing 652
© Jones & Bartlett
Effects Learning,
656 LLC
Heteroplasmy 656
The Genetic Codes of Organelles 653

Contents xiii
Mitochondrial
© Jones & Bartlett Learning, Genetic
LLC © Jones &17.4
Bartlett Learning,
Cytoplasmic LLC
Transmission
Diseases 657
NOT FOR SALE OR DISTRIBUTION NOT FOR SALE of Symbionts 664
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Tracing Population History Through Bacterial Symbionts of Aphids 665
Mitochondrial DNA 658 Killer Strains of Paramecium 666
Cytoplasmic Male Sterility Wolbachia in Arthropods 667
in Plants 659
© Jones & Bartlett Learning, LLC 17.5 Maternal Effect©inJones
Snail & Bartlett Learning, LL
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Respiration-Defective Mitochondrial ROOTS OF DISCOVERY: How the Aphids
Mutants in Yeast 663 Got PVT 665
18 Genes in Populations 677
Learning Objectives & Science Effects of Inbreeding 694
Competencies 678 18.3 Genetics and Evolution 695
18.1 Population Genetics 678
© Jones & Bartlett Learning, LLC © Jones &18.4 Mutation
Bartlett and Migration
Learning, LLC 696
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Random Mating and the
18.5 Random Genetic Drift 698
Hardy–Weinberg Principle 680
Loss of Genetic Variation in Endangered
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Principle ©681 Jones & Bartlett Learning, LLC
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Selection in a Laboratory Experiment 701
Frequency of Heterozygous
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Multiple Alleles 683 Components of Fitness 703
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Typing 684Learning, LLC © Jones & Bartlett
Selection–Mutation Learning,
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Genetic Variation and Linkage 688 Molecular Signals of Selection 706
18.2 Inbreeding 691 ROOTS OF DISCOVERY: A Yule Message from
Dr. Hardy 684
The Inbreeding Coefficient 691
© Jones & BartlettAllelic
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by Descent 692 © Jones &THE CUTTING
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19 Molecular and Human Evolutionary Genetics 717

© Jones
Learning Objectives & Bartlett Learning, LLC
& Science © Jones
Origins of New Genes: & Bartlett Learning, LL
Orthologs
CompetenciesNOT 718 FOR SALE OR DISTRIBUTION and Paralogs 726 NOT FOR SALE OR DISTRIBUT
19.1 Molecular Evolutionary Analysis 718 19.2 Ancient DNA 727
Gene Trees 719 19.3 Where Humans Fit on the Tree of
Bootstrapping 721 Life 729
© Jones
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and Species TreesLLC721 © JonesThat
Evidence & Bartlett
Humans Learning, LLC
Are Most Closely
NOT Molecular
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NOT to
FOR Chimpanzees
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Clock of Evolutionary
Change 722 Similarities in Genomic DNA 729
Rates of DNA Evolution 723 Analysis of Multiple Genetic
Elements 729
Rates of Evolution in Protein-Coding
© Jones & BartlettRegions
Learning,
724 LLC Differences
© Jones & Bartlett BetweenLLC
Learning, Human
and Chimpanzee Genomes 730

xiv Contents
19.4 What Do the Genetic Differences The Denisovan

© Jones & Bartlett Genome
Learning, LLC 742
Between Humans and Chimpanzees 19.7 M
easuring Human Diversity 743
Mean? 732 NOT FOR SALE OR DISTRIBUTION
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to Humans 732
The Apportionment of Within-Group
FOXP2: A Gene Related to Language 733 and Between-Group Variation 746
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Tracing Human History Through
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The Cast of Characters in Human Humans 749
Evolution 735 Amylase and Dietary Starch 749
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Human Origins © Jones &
Adaptation to Bartlett Learning,
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Evolutionary Adaptation Affecting Human
Origins 739 Skin Color 752
Tracing Human History Through THE CUTTING EDGE: The Peopling
Mitochondrial DNA 739 of Western Europe 747
© Jones & BartlettThe
Learning,
NeandertalLLC
Genome 741 © Jones &ROOTS
OF DISCOVERY: Starch Contrast 750
Appendix A: Answers to Even-Numbered Problems 759
Word Roots: Prefixes, Suffixes, and Combining Forms 778
© Genetics
Concise Dictionary of Jones &and
Bartlett Learning,
GenomicsLLC
781 © Jones & Bartlett Learning, LL
Index 808 NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUT


Preface xv
Preface
Students’ curiosity about genetics&

© Jones is refreshed
Bartlettby almost
Learning, ways, we have sought to make
LLC it possible
© Jones for individual
& Bartlett Learning, LL
daily reports in the media of new discoveries related to instructors to customize the order in which they are
NOT FOR SALE OR DISTRIBUTION presented.
genetic differences in drug responses, genetic risk factors
for disease, and genetic evidence for human origins and Our aim is to provide a clear, comprehensive, rigor-
history. They are also intrigued by ethical controversies ous, and balanced introduction to genetics and genom-
related to genetics: Should genetic manipulation be ics at the college level. We believe that a good course
used © onJones
patients&for the treatment of
Bartlett Learning, LLC disease? Should should maintain
© Jonesthe right balance between
& Bartlett Learning, two LLC
impor-
human fetuses be used in research? Should human tant aspects of genetics: (1) genetics as a body of knowl-
edge pertaining to genetic transmission, function, and
beings be cloned? What are the biological and ethical
implications of gene editing? And there are social mutation; and (2) genetics as an experimental
controversies: Should there be laws governing genetic approach, or a kit of “tools,” for the study of biological
privacy? Who should have access to genetic testing processes such as development or behavior. Any stu-
© Jones & records, and for
Bartlett what purpose?
Learning, dent claiming
LLC What is the proper role© Jones & Bartletta knowledge
Learning, of genetics
LLC must achieve the
of direct-to-consumer genotyping services? following milestones:
The teacher of genetics, in turn, faces myriad ■■ Understand the basic processes of gene transmis-
challenges: sion, mutation, expression, and regulation

■■ Sustaining students’ enthusiasm about this topic ■■ Be familiar with the principal experimental
■■ Motivating their desire to understand the prin- methods that geneticists and molecular biolo-
ciples of genetics in a comprehensive and rigor-
LLC © Jones
gists use in their studies, and& recognize
Bartlett Learning,
the LL
ous way NOT FOR SALE OR DISTRIBUTION advantages and limitations NOT FOR SALE
of these OR DISTRIBUT
approaches
■■ Think like a geneticist at the elementary level of
■■ Guiding students in gaining an understanding
that genetics is not only a set of principles but being able to formulate genetic hypotheses,
also an experimental approach to solving a wide work out their consequences, and test the results
against observed data
©range
Jones of biological
& Bartlett problems
Learning, LLC © Jones & Bartlett Learning, LLC
■■ State genetic principles in his or her own words
■■ Helping students learn to think about genetic
problems and about the wider social and ethical and recognize the key terms of genetics in
issues arising from genetics and genomics context
■■ Solve problems of several types, including single-
Genetics: Analysis of Genes and Genomes, Ninth
Edition, addresses these challenges while emphasizing concept exercises that require application of
© Jones & theBartlett Learning,
beauty, logical and unity of the subject. Our© Jones &definitions
clarity, LLC or the basic LLC
Bartlett Learning, principles of genetics,
NOT FORpedagogical
SALE ORapproach
DISTRIBUTION problems in genetic
is to treat transmission genetics,NOT FOR SALE OR DISTRIBUTION analysis in which several
molecular genetics, and evolutionary genetics as fully concepts must be applied in logical order, and
integrated subjects. This integration appeals to most problems in quantitative analysis that call for
some numerical calculation
modern geneticists, who recognize that the distinctions
■■ Gain some sense of the social and historical con-
between the subfields are artificial. The chapters in this
text have been arranged into five sections: an overall LLC text in which genetics © Jones & Bartlett
and genomics Learning, LL
has devel-
introduction to genes and genetic analysis, transmission oped and is continuing
NOT to develop
genetics, the organization and replication of DNA, gene ■■ Acquire a basic familiarity with the genetic
expression and regulation, and evolutionary genetics. resources and information that are available
Recognizing that these topics can be organized in many through the Internet

xvi The Student Experience
The Student Experience

We have included many special&features

© Jones to help
Bartlett stu-
Learning, LLC © Jones & Bartlett Learning, LL
dents achieve these learning goals. The text is clearly
and concisely written in a student-friendly and relaxed
prose style.
Each chapter begins with an explicit statement of

■■
©the Learning Objectives and Science Competencies

Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC
that students should aim to achieve. These guide-
NOT FOR SALE OR
posts are intended DISTRIBUTION
to help students identify key NOT FOR SALE OR DISTRIBUTION
concepts and use them at a variety of learning levels,
including comprehension, application, analysis, and
synthesis. They also serve as powerful study tools
when reviewing the material for course and exam
preparation. ©
A unique feature of this text is the Roots of

■■
Discovery boxes. Each chapter contains one or two

© Jones & Bartlett Learning, LLC of these boxes, in which the text&material
© Jones Bartlett is con-
Learning, LL
nected to excerpts from classic papers that report
NOT FOR SALE OR DISTRIBUTION key experiments in NOT FOR
genetics or SALE OR DISTRIBUT
raise important
social, ethical, or legal issues in genetics. Each Roots
of Discovery feature includes a brief introduction
explaining the importance of the experiment and
the historical context in which it was carried out,
followed & excerpts
by short BartlettfromLearning,
the originalLLC
litera-
NOT FOR SALE OR DISTRIBUTION tureNOT FOR SALE OR DISTRIBUTION
of genetics, interspersed with commentary
connecting the results and conclusions of the paper
to the topics covered in the chapter. Many of these
boxes offer excerpts from historical papers, such as
Mendel’s paper, but by no means are they all “old”
papers. Indeed, many of these “classic” papers are
© Jones & Bartlett Learning, LLC © Jones &very Bartlett
recent. Learning, LLC
NOT FOR SALE OR DISTRIBUTION NOT FOR Some of theOR
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pieces were published originally in French,
others in German. These excerpts appear in English transla-
tion. In papers that use outmoded or unfamiliar terminology,
or that use archaic gene symbols, we have substituted the
modern equivalent because the use of a consistent termi-
nology in the text and in the©Roots Jones & Bartlett
of Discovery Learning, LL
features
makes the material more accessible to the student.

The Student Experience xvii
In addition, several chapters contain Cutting Edge

© Jones &students
Bartletta taste of where it is going. Each of these
Learning, LLC
■■
boxes, which are designed to introduce students to features focuses on recent work that has the poten-
NOT FOR SALEsomeOR of DISTRIBUTION NOT
the more innovative work being done in the FOR SALE OR DISTRIBUTION
tial to be transformative in the future or that has
field. Topics such as the bacterial genetics of introduced new methods of analysis that can be
CRISPR–Cas9, genome-wide association studies applied to questions in genetics and genomics.
based on personal genomics, and the potential of Each also includes references to the original work
gene drive are designed to help students appreciate that can be incorporated into class activities and
© Jones
the advances being made at&the
Bartlett
forefront Learning,
of genet- LLC assignments. We hope©that
Jones & Bartlett
the Cutting Learning, LL
Edge feature
ics. While the Roots
NOT of Discovery
FOR SALE boxes OR DISTRIBUTION will prove both usefulNOT
are designed and stimulating,
FOR SALE and that
ORthe DISTRIBUT
to highlight the experimental foundations of genet- format we have used can be applied to other new
ics, the Cutting Edge boxes are intended to give advances as they occur.



xviii The Student Experience
The art program is spectacular and a learning aid

■■ Characteristic colors and shapes have been used
❍❍
© Jones & Bartlett
in itself.Learning,
Every chapterLLC
© Jones & Bartlett
is richly illustrated with beau-
Learning, LLC
consistently throughout the text to indicate dif-
NOT FOR SALEtifulOR DISTRIBUTION
graphics in which color is used functionally to NOT FOR SALE OR DISTRIBUTION
ferent types of molecules—DNA, mRNA, tRNA,
enhance the value of each illustration as a learning and so forth. For example, DNA is illustrated in
aid. The illustrations are also heavily annotated with any one of a number of ways, depending on the
explanatory boxes explaining in a step-by-step level of resolution necessary for the illustration,
fashion what is happening at each level of the illus- and each time a particular level of resolution is
© Jones
tration. These labels make the& Bartlett
art inviting Learning,
as well as LLC depicted, the DNA©isJones
shown in&theBartlett
same way.Learning,
A LL
informative. TheyNOTalso allow
FORthe illustrations
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OR DISTRIBUTION great deal of potential
NOTconfusion
FOR SALE is avoided by
OR DISTRIBUT
relatively independently of the text, enabling stu- ensuring that DNA, RNA, and proteins are repre-
dents to review material without rereading the sented in the same manner in every chapter.
whole chapter. The art program is used not only for ❍❍ Numerous full-color photographs feature molec-
its visual appeal but also to increase the pedagogi- ular models in three dimensions; these give a
cal value of the text. strong visual&reinforcement of the concept
© Jones & Bartlett Learning, LLC © Jones Bartlett Learning, LLCof
macromolecules as physical entities with defined
three-dimensional shapes and charge distribu-
tions that serve as the basis of interaction with
other macromolecules.
❍❍The page design is clean, crisp, and uncluttered.
As a result, the text is pleasant to look at and easy
to read.
Learning, LLC



The Student Experience xix

NOT FOR SALE OR DISTRIBUTION ■■ NOTstudents
To help FOR SALE OR
focus on theDISTRIBUTION
key details of this
challenging subject, each numbered section con-
cludes with a Summing Up feature that highlights
the most important concepts. Then, at the end of
each chapter, a Chapter Summary in bulleted list
© Jones & Bartlett Learning, LLC © Jones &form
Bartlett
collectsLearning,
key learningLLC
points for students.
■■ Each OR DISTRIBUTION
chapter concludes with approximately 50
problems for solution, graded in difficulty, for the
students to test their understanding. The problems
are of several different types.

❍❍ Review the Basics questions review the major
concepts by presenting questions for discussion.
These questions ask for genetic principles to be
restated in the student’s own words; some are
© Jones & Bartlett Learning, LLC © or
matters of definition Jones
call for &
theBartlett Learning,
application of LL
elementary principles.

xx The Student Experience
The Guide to Problem Solving demonstrates

❍❍
typical problems that apply the principles. The
NOT FOR SALE problems are worked in full, showing the con-NOT FOR SALE OR DISTRIBUTION
OR DISTRIBUTION
cepts needed to solve the problem and the
reasoning behind the answer. This feature serves
as a review of the important concepts used in
working problems. It also highlights some of the
most common © Jones
mistakes& made
by beginning © Jones & Bartlett Learning, LL
students andNOTgives FOR
pointers on how
SALE ORthe DISTRIBUTION
student NOT FOR SALE OR DISTRIBUT
can avoid falling into these conceptual traps.
A large number of Analysis and Applications
❍❍
problems are provided (with answers to even-

numbered problems at the end of the text). In
© Jones & Bartlett
these more Learning,
traditional LLC prob-
types of genetic © Jones & Bartlett Learning, LLC
lems, several concepts must be applied in logi-
NOTcalFOR SALE OR DISTRIBUTION
order and some numerical calculation may
be required. The level of mathematics is that of
arithmetic and elementary probability as it per-
tains to genetics. None of the problems uses
mathematics beyond elementary algebra.


❍❍Challenge Problems are similar to the Analysis

and Applications problems but are more chal-
© Jones & often
lenging, Bartlett Learning,
because LLCa more
they require © Jones & Bartlett Learning, LLC
NOTextensive
FOR SALE OR
analysis of DISTRIBUTION
data before the question NOT FOR SALE OR DISTRIBUTION
can be answered.

The Student Experience xxi
At the end of the text are Answers to Even-

■■
Numbered Problems, in which the logic of each
NOT FOR SALE explained in full. The answers are complete,NOT FOR SALE OR DISTRIBUTION
ORisDISTRIBUTION
answer
explaining the logical foundation of the solution and
laying out the methods used. We find that many of
our students, like students everywhere, often sneak
a look at the answer before attempting to solve a
problem. This is©a Jones & Bartlett
pity. Working backwardLearning,
from the LLC © Jones & Bartlett Learning, LL
answer should NOTbe a last
FORresort,
SALEbecause
ORproblems
are valuable opportunities to learn. Problems that
the student cannot solve are usually more important
than the ones that the student can solve, because
the sticklers usually identify trouble spots, areas of
©confusion,
Jones &orBartlett
gaps in understanding. Therefore, we
Learning, LLC
urge our students to try to answer each question
NOT FOR SALE OR
before looking at the answer.DISTRIBUTION
The answers to the NOT FOR SALE OR DISTRIBUTION
odd-numbered questions are provided to the
instructor as part of the Teaching Tools package so
they could be assigned for a grade.
■■ At the end of the text, we include a short list of Word
© Jones & Bartlett
Roots Learning,
that are used LLC
in many of the technical terms© Jones & Bartlett Learning, LLC
of genetics. The Word Roots are intended to helpNOT FOR SALE OR DISTRIBUTION
students interpret and remember the meaning of
key terms, and master the essential terminology of
genetics and genomics.

NOT FOR SALE OR DISTRIBUTION NOT
■■ The Concise Dictionary of FOR SALE
Genetics foundOR DISTRIBUT
at the
end of the text enables students to check their
understanding of the key words or look up any
technical terms they may have forgotten. It includes
not only the key words but also genetic terms that
students & Bartlett
are likely Learning,
to encounter LLCthe
in exploring
Internet or in their further reading.


xxii What’s New in the Ninth Edition?
What’s New in the

Ninth Edition?
This edition has been completely revised and updated. called Review the Basics, a Guide to Problem Solving,
Each chapter has been thoroughly reworked, and the problems for solution in a section called Analysis and
organization of topics, as reflected in the order of chap- Applications, and Challenge Problems.
ters, has been revised. To a great
© Jones & Bartlett Learning, LLCextent, this reorganiza- © Jones & Bartlett Learning, LLC
tion was driven bySALE
developments in the field—especially Contents and Organization
NOT FOR OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION
Today, most students learn about DNA in grade school
the explosion of data being generated by high-through-
put DNA sequencing, particularly in humans. These or high school; in our teaching, we have found it artifi-
advances have revolutionized the study of genetic varia- cial to pretend that DNA does not exist until the middle
tion in populations and brought genome-wide associa- of the term. Thus, an important feature is the presence
tion
© Jones & studiesLearning,
Bartlett (GWAS) and LLC related methods to the© Jones of two&introductory chapters providing
Bartlett Learning, LLC a broad over-
forefront. The subject of GWAS is introduced in the con- view of DNA, genes, and genomes—what they are, how
text of gene mapping (Chapter 5) and expanded upon they function, how they change by mutation, and how
with respect to the genetics of complex traits (now they evolve through time. The introductory chapters
Chapter 7). Other applications of high-throughput serve to connect the more advanced concepts that stu-
approaches to genetics include greatly expanded cover- dents are about to learn with what they already know.
age of RNA-seq (Chapter 14), cancer
© Jones genomics Learning,
& Bartlett (Chapter They also serve to provide©each
LLC Jonesstudent with a solid
16), and ancient DNANOT analysis (Chapter 19). framework for integrating the material that comes later.
FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUT
Roots of Discovery boxes (formerly Connections An important role they play is to provide a sufficient
boxes) have been rewritten, in most cases reducing the grounding in the molecular basis of genetics—DNA
extent of direct quotes from the original papers and pro- structure and replication, as well as the central dogma
viding readers with focused connections to the major of molecular biology—so that molecular concepts can be
points©ofJones
the topic
&being covered.
Bartlett All Roots LLC
Learning, of Discovery integrated© into chapters
Jones covering “classical”
& Bartlett Learning, topics
LLCsuch
boxesNOTcontain complete citations of the papers profiled, as Mendelian genetics and gene mapping.
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including URLs, so that they can easily be explored in Throughout each chapter, there is a balance
more depth, either by the interested student or as part of between observation and theory, between principle and
an instructor-designed activity. Cutting Edge boxes, a concrete example, and between challenge and motiva-
new feature, also provide connections to the literature tion. Molecular, classical, and evolutionary genetics are
to facilitate further exploration. integrated throughout the text. Frequent references are
made to human genetics. The text is also liberally popu-
NOT FORChapter
Organization NOT FOR SALE
lated with OR DISTRIBUTION
applications to other animals and plants,
To help students keep track of the main issues and avoid including the key model organisms used in genetics and
being distracted by details, each chapter opens with an genomics.
Outline that shows the road map of the territory ahead. Next, we describe some of the highlights of the five
This is followed by a list
© Jones & Bartlett Learning, LLC sections of the text. © Jones & Bartlett Learning, LL
of Learning Objectives and Sci- major
ence Competencies identifying the most important con-
cepts and principles.NOT FOR SALE
An opening paragraphORgives
DISTRIBUTION
an Defining and Working with NOT
GenesFOR SALE OR DISTRIBUT
overview of the chapter, illustrates the subject with ■■ Genes, Genomes, and Genetic Analysis (Chapter 1) is
some specific examples, and shows how the material is an overview of genetics designed to bring stu-
connected to genetics as a whole. The text makes liberal dents with disparate backgrounds to a common
use of©numbered and bulleted lists
Jones & Bartlett Learning, LLC to help students orga- level
©ofJones
understanding.
& BartlettThis Learning,
chapter enables
LLCclas-
nize their learning, as well as summary statements set sical, molecular, and evolutionary genetics to be
off in special type to emphasize important principles.
integrated in the rest of the text. Included in this
Each numbered section concludes with a bulleted list chapter are the basic concepts of molecular genet-
entitled “Summing Up,” which highlights the major ics: DNA structure, replication, expression, and
points covered in the section and will help the student mutation. A feature of this chapter is a detailed
review and master the
© Jones & Bartlett Learning, LLC material covered. Each chapter © Jones &exploration of the work ofLLC
Bartlett Learning, Beadle and Tatum that
ends with a Chapter Summary, questions for discussion led to the one-gene-one-enzyme hypothesis and

What’s New in the Ninth Edition? xxiii
the use of complementation analysis as a tool for© Jones &experimental organisms,LLC

Bartlett Learning, has been retained, as
genetic inference has streamlined coverage of tetrad analysis in
NOT FOR SALE OR DISTRIBUTION NOT FOR fungi.
SALENew ORtoDISTRIBUTION
the ninth edition is a section on
■■ DNA Structure and Genetic Variation (Chapter 2)
emphasizes that the primary tools of the modern genetic mapping in humans, which includes
geneticist are methods for the experimental expanded coverage of lod score analysis of pedi-
manipulation of DNA. It includes a more grees, as well as an entirely new section on gene
detailed look at©DNAJones & Bartlett Learning, LLC localization by association
structure, and it introduces © Jones analysis.
the principal methods of DNA manipulation,
NOT FOR SALE OR DISTRIBUTION ■■ Human Karyotypes and Chromosome Behavior
including restriction enzymes, electrophoresis, (Chapter 6) covers the principles of chromosome
DNA hybridization, Southern blotting, and the mechanics with special reference to human
polymerase chain reaction (PCR). We also intro- chromosome number and structure and the
duce single-nucleotide polymorphisms (SNPs) types of aberrations that are found in human
and copy-number polymorphisms
© Jones & Bartlett Learning, LLC (CNPs) and chromosomes.
© Jones &The genetic implications
Bartlett Learning, ofLLCchro-
discuss how these types
NOT FOR SALE OR DISTRIBUTION of genetic markers can mosome abnormalities—duplications,
NOT FOR SALE OR DISTRIBUTION deficien-
be assayed on a genome-wide scale using oligo- cies, inversions, and translocations—are also
nucleotide microarrays (DNA chips). The use of discussed. The evolutionary significance of gene
simple-sequence repeat variation for genotyping duplication is introduced, and the genetic con-
is given expanded coverage. sequences of translocation heterozygosity (pseu-
© Jones & Bartlett Learning, LLC © Jones &dolinkage)
Bartlett is Learning,
described. LLC
Transmission Genetics
■■ The ORBasis
Genetic DISTRIBUTION
of Complex Traits (Chapter 7)
■■ Mendelian Genetics: The Principle of Segregation and covers quantitative genetics. It is a revision of
Assortment (Chapter 3) introduces the fundamen- Chapter 18 from the previous edition. We chose
tal Mendelian concepts of random segregation to introduce this material earlier because of the
and independent assortment, not only as they growing importance of genome-wide association
can be inferred ©from
Jones & Bartlett
crosses involvingLearning,
experi- LLC studies in both agriculture © Jones & Bartlett
and medicine. Learning, LL
Crohn’s
mental organisms NOT FOR
like peas SALE
and flies,OR butDISTRIBUTION
also by NOT for
disease is used as a model FOR SALE
doing so, andOR DISTRIBUT
both
analysis of human pedigrees. The role of proba- the strengths and weaknesses of GWAS as a tool
bility in genetic analysis is also introduced. A are highlighted. Coverage of heritability has been
unique feature of this chapter is the integration of revised, and a new section on misconceptions
molecular genetics with Mendel’s experiments. about it has been added.
©WeJones & Bartlett
describe Learning,
the molecular LLC
basis of the wrinkled © Jones & Bartlett Learning, LLC
■■ Genetics of Bacteria and Their Viruses (Chapter 8)
NOT FOR and
mutation SALE show OR DISTRIBUTION
how a modern geneticist NOTthe
extends FOR use SALE ORanalysis
of genetic DISTRIBUTION
to bacteria
would carry out Mendel’s study, examining the (mainly Escherichia coli) and viruses, and serves
molecular phenotypes on the one hand and the as a transition into the more molecular subjects
morphological phenotypes on the other hand. covered in subsequent chapters. The section on
This pedagogy provides a solid basis for under- plasmids has been revised to focus more specifi-
standing LLC
not only Mendel’s experiments as he© Jones &cally Bartlett
on theLearning, LLC detailed coverage
F plasmid; more
actually performed and interpreted them, butNOT FOR of SALE OR DISTRIBUTION
bacterial plasmids in general has been moved
also the use of modern molecular approaches in to the Molecular Organization of Chromosomes and
genetic analysis. Molecular markers are also inte- Genomes chapter. Some of the classical experi-
grated into human genetic analysis. ments and methods, such as replica plating and
■■ The Chromosomal Basis of Inheritance (Chapter 4) the “U-tube” experiment, are highlighted. The
covers the cell© Jones
cycle, & Bartlett
mitosis and meiosis,Learning,
and LLC description of the origin © Jones & Bartlett
of the term Learning, LL
“cistron” and
NOT FOR SALE OR
hypothesis testing in genetics. The approach to DISTRIBUTION NOT FOR SALE OR
the cis-trans test has been expanded, and CRISPR– DISTRIBUT
the chi-squared test has been revised by introduc- Cas9 as a bacterial system is introduced in a
ing random variables and their distributions, Cutting Edge box.
first with respect to the binomial distribution and
then with respect to the chi-squared distribution. Organization and Replication of Chromosomes
© Computer-simulated
Jones & Bartlett distributions
Learning, LLC are used to and DNA
illustrate the logic of significance testing, after NOT FOR SALE OR DISTRIBUTION
■■ Molecular Organization of Chromosomes and Genomes
which the mechanics of actually performing a (Chapter 9) continues the transition into the
chi-squared test are described. molecular basis of inheritance, covering the orga-
■■ Genetic Linkage and Chromosome Mapping (Chapter
nization of DNA in the genomes of both prokary-
5) covers linkage
© Jones & Bartlett Learning, LLC analysis and gene mapping. © Jones &otes and eukaryotes.
Bartlett Learning, LLC It now includes an
The classical approach, involving test crosses in
NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTIONin both types of
introduction to mobile DNA

xxiv What’s New in the Ninth Edition?
organisms. The section on Cot kinetics has been© Jones &CRISPR–Cas9. Included are
Bartlett Learning, LLCthe use of restriction
shortened, recognizing that while historically enzymes and vectors in recombinant DNA, clon-
and conceptually important, this methodology
NOT FOR SALE
ing OR DISTRIBUTION
strategies, site-directed mutagenesis, the
is no longer in active use. The description of chro- production of genetically defined transgenic
mosome condensation has been updated, and its animals and plants, and applications of genetic
connection to mitosis (and meiosis) has been engineering. Coverage of whole-exome sequenc-
made more explicit.
© Jones & Bartlett Learning, LLC ing has been expanded,
© Jonesand a&new sectionLearning,
Bartlett on LL
■■ DNA Replication and Sequencing (Chapter 10)covers functional genomics has been added. This mate-
NOT FOR SALE OR DISTRIBUTION rial includes expanded NOT FOR SALE OR
coverage of RNA-seq and
DISTRIBUT
the mechanics of DNA replication and methods
of sequencing as the starting point for an in-depth a description of quantitative PCR for transcript
discussion of the molecular basis of genetics. The quantification. A subsection on use of RNAi for
mechanisms of DNA replication are described first gene expression knockdown has been added, as
©for
Jones & Bartlett
prokaryotes and thenLearning, LLC
for eukaryotes. Coverage has a major section on gene editing
© Jones & Bartlett Learning, with CRISPR–
LLC
of Sanger Cas9. Associated with the latter is a Cutting Edge
NOT FORsequencing
SALE OR is followed by a description
box on the use of these methods in a mouse
of sequencing-by-synthesis, using the Illumina
platform as a model. model of muscular dystrophy.
■■ Genetic Control of Development (Chapter 15) focuses
Mutation, Repair, and Recombination (Chapter 11)
■■
covers mutation, DNA repair, and recombina- on genetic analysis of development in nema-
tion. In previous editions, mutation was pre- © Jones & Bartlett
todes Learning,
(Caenorhabditis LLCand Drosophila and
elegans)
NOT FOR SALE OR DISTRIBUTION includes a thorough examination of the genetic
sented in a later chapter, but by having itNOT FOR SALE OR DISTRIBUTION
basis of floral development in Arabidopsis thali-
immediately follow coverage of DNA replication,
ana. A new section on the role of regulatory
we hope to emphasize the importance of all of
RNAs in the control of development has been
these processes in both the maintenance of
added, including examples from nematodes,
genetic continuity and the generation of new
variation. Coverage of the classical Luria–
LLC flies, and mammalian © Jones & Bartlett Learning, LL
Hox genes.
NOT FOR
Delbruck experiment, SALE
showing thatOR DISTRIBUTION
mutation is ■■ Molecular Genetics of NOT FORCycle
the Cell SALE and OR DISTRIBUT
Cancer
random with respect to adaptation, has been (Chapter 16) investigates cancer from the stand-
added. Coverage of mechanisms of recombina- point of the genetic control of cell division, with
tion has been incorporated in this chapter, emphasis on the checkpoints that, in normal
emphasizing the similarity between these mecha- cells, result either in inhibition of cell division or
©nisms
and post-replication repair mechanisms.
© Jones & cell
in programmed Bartlett
death Learning, LLC
(apoptosis). Cancer
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results FOR
from SALEofOR
a series DISTRIBUTION
successive mutations,
Gene Expression usually in somatic cells that overcome the nor-
mal checkpoints that control cellular prolifera-
■■ Molecular Biology of Gene Expression (Chapter 12)
tion. A new section on cancer genomics has been
covers the processes of transcription, translation, added, using pancreatic cancer as a model for
and RNA
© Jones & Bartlett processing.
Learning, Transcription mechanisms© Jones &characterization
LLC Bartlett Learning, LLC
of the mutational and transcrip-
in prokaryotes and eukaryotes are more clearly
NOT FOR SALE OR DISTRIBUTION NOT FOR tisomal
SALE OR changes that are associated with tumor
DISTRIBUTION
differentiated; the concept of consensus progression.
sequences is introduced more comprehensively,
along with visualizations of them as “sequence Variation
logos.” ■■ Mitochondrial DNA and Extranuclear Inheritance
© Jones
Molecular Mechanisms
■■ & Bartlett
of Gene Regulation Learning,
(Chapter LLC (Chapter 17) covers non-nuclear
© Jones & Bartlett
genetics, Learning, LL
includ-
13) covers theNOTregulation
FOR of SALEgene OR
expression.
DISTRIBUTION ing genetic defectsNOT FOR SALE
in human OR DISTRIBUT
mitochondrial
Mechanisms in prokaryotes and eukaryotes have DNA. A new section has been added that
been separated, so that they can be better com- describes the transmission of Wolbachia in
pared and contrasted. The section on the role arthropods.
played by noncoding RNAs in regulation has been ■■ Genes in Populations (Chapter 18) covers popula-
© expanded,
Jones & highlighting
Bartlett Learning,
their roles LLC
in processes © Jones & Bartlett Learning, LLC
tion genetics (material on molecular evolution
NOTsuchFOR SALE OR DISTRIBUTION
as X-chromosome inactivation, alternative hasNOT
been FOR
moved SALE
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Molecular and Human
mRNA splicing, and translational regulation. Evolutionary Genetics chapter). The section on
■■ Manipulating Genes and Genomes (Chapter 14) DNA fingerprinting has been updated to illus-
covers experimental methods of gene manipula- trate use of short tandem repeats as markers. A
tion, beginning with the classical methods of new subsection on linkage disequilibrium has
gene cloning and proceeding forward to genomic
© Jones &been
added, along with “heat map” illustrations
analysis, transcriptomics, and gene editing with NOT FOR SALE OR DISTRIBUTION
of disequilibrium derived from genomic data. In

What’s New in the Ninth Edition? xxv
the discussion of evolutionary processes, the© Jonesmolecular and classical

& Bartlett principles
Learning, LLCthroughout the text,
order of topics has been rearranged so that so you can begin a course with almost any of the chap-
NOT FOR SALE OR drift—a
genetic random process found in all finiteNOT ters.
DISTRIBUTION FORMostSALE OR DISTRIBUTION
instructors will prefer to start with the over-
populations—is addressed prior to examining the view in the Genes, Genomes, and Genetic Analysis chapter
deterministic process of natural selection. A new because it brings every student to the same basic level of
section on molecular signals of selection has understanding. The DNA Structure and Genetic Variation
been added, incorporating material on lactase
© Jones & Bartlett Learning, LLC chapter introduces the basic experimental
© Jones manipula-
persistence in humans. A Cutting Edge box tions used in modern genetics and serves to integrate
describes the principles of “gene drive” based on
NOT FOR SALE
molecular and classical genetics in the discussion of
OR DISTRIBUT
CRISPR–Cas9 and explains how it might be used Mendel in the Transmission Genetics: The Principle of Seg-
to control mosquito vectors of malaria. regation chapter. Some other approaches that instructors
■■ Molecular and Human Evolutionary Genetics (Chap- might use to structure the beginning of their course are
ter 19) covers both molecular
© Jones & Bartlett Learning, LLC and human evolu- outlined here.
tion, since most of the advances
NOT FOR SALE OR DISTRIBUTION in the latter have NOT FOR SALE OR DISTRIBUTION
resulted from developments in the former. Other Approach Chapters to begin with
changes in this chapter include an expanded Mendel-early Genes, Genomes, and Genetic Analysis
section on ancient DNA analysis and the use of format
Alu1 insertion sites to resolve hominid phylog- Transmission Genetics: The Principle of
Segregation
eny. Coverage LLC in the genus Homo has© Jones & Bartlett Learning, LLC
of diversity
NOT FOR SALE beenORrevised to include new findings about H.NOT FOR SALE OR
DISTRIBUTION DNA Structure and Genetic Variation
DISTRIBUTION
denisova and H. floresiensis. The section on genetic Chromosome- Genes, Genomes, and Genetic Analysis
variation in H. sapiens has been revised to incor- early format
Chromosomes and Sex-Chromosome
porate data from the 1000 Genomes Project (as Inheritance
opposed to HapMap in previous editions) and to
DNA Structure and Genetic Variation
include the use©ofJones
genetic&assignment
Bartlett Learning,
methods LLC © Jones & Bartlett Learning, LL
(“STRUCTURE”) for characterization of
NOT FOR SALE OR DISTRIBUTION modern Transmission NOT FOR
Genetics: SALE
The Principle of OR DISTRIBUT
human variation. A new Cutting Edge box Segregation
focuses on use of ancient DNA genotyping to Genetic Linkage and Chromosome Mapping
characterize the peopling of Western Europe.
Genomes-first Genes, Genomes, and Genetic Analysis
format
Flexibility
DNA Structure Learning,
and Genetic Variation LLC
ThereNOT
is no FOR
requirement
SALEtoOR
startDISTRIBUTION
at the beginning of this NOTChromosomes
and Sex-Chromosome
text and proceed straight to the end. In fact, doing so in Inheritance
a typical one-semester course borders on the impossible.
In this ninth edition, each chapter has been designed to The writing and illustration program were designed
be a self-contained unit that stands on its own. This fea- to accommodate a variety of formats, and we encourage
ture
© Jones & gives instructors
Bartlett Learning,the option
LLCof using whatever order© Jonesteachers to take advantage
& Bartlett of thisLLC
Learning, flexibility to meet their
suits them, and of skipping particular chapters that do own unique needs.
NOT FORnotSALE OR DISTRIBUTION
fit with their course design. We have integrated


xxvi Teaching Tools
Teaching Tools
Jones & Bartlett Learning offers a suite

© Jones of traditional
& Bartlett and
Learning, LLC ■■ A PowerPoint presentation
© Jones &containing the
Bartlett Learning, LL
interactive multimedia supplements to assist instructors detailed outline for each chapter of Genetics:
NOT FOR SALE OR DISTRIBUTION Analysis of Genes andNOT FOR SALE OR DISTRIBUT
Genomes, Ninth Edition, is
and aid students in mastering genetics. Additional infor-
mation and review copies of any of the following items included. This presentation, which is designed
are available through your Jones & Bartlett Learning to mirror the text, is constructed flexibly to meet
sales representative. your lecture’s organization. The outline is open,
■© Jones & Bartlett Learning, allowing you to&provide the Learning,
elements youLLCdeem
■ The PowerPoint Image Bank is anLLC easy-to-use © Jones Bartlett
necessary, whether it be new text or more images
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from the Image Bank.
tions and photos from the text (to which Jones &
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electronically) for use in classroom presentation.
You can select images you need or easily generate
your own LLCor you can print the files© Jones & Bartlett Learning, LLC
slide shows,
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■■ A Test Bank containing more than 1,000 ques-
tions and complete answers is available. The
questions are a mix of factual, descriptive, and
© Jones & Bartlett Learning, LLC © Jonestypes.
quantitative & Bartlett Learning,
A typical LLC
chapter contains
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Microsoft Word documents.

Teaching Tools xxvii
■■ The Instructor’s Manual includes Chapter

Summaries, Teaching Tips, References,
Suggested Activities, and more.




xxviii Acknowledgments
Acknowledgments
We are indebted to many colleagues

© Jones whoseLearning,
& Bartlett advice, Leslie Dendy, University of©
LLC New Mexico,
Jones Los Alamos,
thoughtful reviews, and comments have helped in the NM
preparation of this and previous editions. Their expert Stephen J. DíSurney, University of Mississippi,
recommendations are reflected in the content, organiza- Oxford, MS
tion, and presentation of the material.
Laura Adamkewicz, George Mason University, John W. Drake, National Institute of Environmental
© Jones
Fairfax, VA & Bartlett Learning, LLC Health Sciences,
© JonesResearch Triangle Learning,
& Bartlett Park, NC LLC
Jeremy C. Ahouse, Brandeis University, Waltham, Kathleen NOT
Dunn, FOR
BostonSALE
College,OR DISTRIBUTION
Boston, MA
MA Chris Easton, State University of New York, Bingham-
Mary Alleman, Duquesne University, Pittsburgh, PA ton, NY
Peter D. Ayling, UniversityLLC

of Hull, Hull, United Joel C. Eissenberg, St. Louis University, St. Louis, MO
© Jones & Bartlett Learning, © Jones & Bartlett Learning, LLC
Kingdom
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Lafayette, IN Brian E. Fee, Manhattan College, Riverdale, NY
© University,
Mary K. B. Berlyn, Yale Jones & Bartlett
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CT LLC © Jones
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University, Learning, LL
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David Botstein, Princeton University, Princeton, NJ
Colin G. Brooks, The Medical School, Newcastle, Matthew K. Fujita, University of Texas at Arlington,
United Kingdom Arlington, TX
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AZ
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AL Kent G. Golic, University of Utah, Salt Lake City, UT
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Lincoln, NE Jeffrey C. Hall, Brandeis University, Waltham, MA
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Acknowledgments xxix
© Jones Ivan Huber, Fairleigh Dickinson University, Madison,© Jones

& Bartlett Learning, LLC Ronald
& L. Phillips,Learning,
Bartlett University ofLLC
Minnesota, St. Paul,
NJ MN
Kerry Hull, Bishop’s University, Quebec, Canada David Pilbeam, Harvard University, Cambridge, MA
Lynn A. Hunter, University of Pittsburgh, Pittsburgh, Robert Pruitt, Purdue University, West Lafayette, IN
PA
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About the Authors xxxi
About the Authors

Daniel L. Hartl is Higgins Professor

© Jones of Biology
& Bartlett at Har-
Learning, Bruce J. Cochrane is Professor
LLC © Jonesof Biology at Miami
vard University and NOT
a member of the National Acad- University. He received his BA in biology at Cornell
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University and his PhD in genetics at Indiana Univer-
emy of Sciences and the American Academy of Arts
and Sciences. He received his BS and PhD from the sity, and carried out postdoctoral research at the Uni-
University of Wisconsin and carried out postdoctoral versity of North Carolina. His research interests
research at the University of California at Berkeley. His include population genetics, evolutionary biology,
research interests include molecular
© Jones & Bartlett Learning, LLC genetics, genom- and bioinformatics.
ics, molecular evolution, and population
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NINTH EDITION

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LL

ANALYSIS OF GENES AND

Bruce J. Cochrane, PhD

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LL

© Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION.

© Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION.

Unit I Defining and Working

2 DNA Structure and Genetic Variation 40

Unit II Transmission Genetics 81

Unit III Organization

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Unit I Defining and Working with GENES 1

2 DNA Structure and Genetic Variation 40

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The Polymerase Chain Reaction 60 © Jones &2.7Bartlett

Unit II Transmission Genetics 81

4 The Chromosomal Basis of Inheritance 120

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4.5 Probability in the Prediction The Chi-Square

5 Genetic Linkage and Chromosome Mapping 159

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Deletion Mapping 218 Pseudolinkage

8 Genetics of Bacteria and Their Viruses 279

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8.4 Genetic Exchange and Conjugation 286 Fine Structure

9 Molecular Organization of Chromosomes and Genomes 320

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10.5 Terminating Replication 367 © Jones &10.7 Exploiting

11 Mutation, Repair, and Recombination 382

Unit IV Gene Expression 423

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12.5 Transcription in Eukaryotes 433 InitiationLearning,

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13.9 Translational Control 505 Mating-Type

14 Manipulating Genes and Genomes 519

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Epistasis in the Analysis of ­Developmental Homeotic Genes 592

17© Mitochondrial DNA and Extranuclear Inheritance

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19 Molecular and Human Evolutionary Genetics 717

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19.4 What Do the Genetic Differences The Denisovan

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Students’ curiosity about genetics&

challenges: sion, mutation, expression, and regulation

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The Student Experience

We have included many special&features

Each chapter begins with an explicit statement of

©the Learning Objectives and Science ­Competencies

A unique feature of this text is the Roots of

­Discovery boxes. Each chapter contains one or two

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In addition, several chapters contain Cutting Edge

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LL

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The art program is spectacular and a learning aid

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LL

© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LL

4.5 Probability in the Prediction The Chi-Square

10.5 Terminating Replication 367 © Jones &10.7 Exploiting

Unit IV Gene Expression 423

13.9 Translational Control 505 Mating-Type

Epistasis in the Analysis of Developmental Homeotic Genes 592

19.4 What Do the Genetic Differences The Denisovan

©the Learning Objectives and Science Competencies

Discovery boxes. Each chapter contains one or two

At the end of the text are Answers to Even-