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E-grāmata: Primer of Population Genetics and Genomics

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(Higgins Professor of Biology, Department of Immunology and Infectious Diseases, Harvard University, USA)
  • Formāts: 272 pages
  • Izdošanas datums: 18-Jun-2020
  • Izdevniecība: Oxford University Press
  • Valoda: eng
  • ISBN-13: 9780192607041
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Primer of Population Genetics and GenomicsPalielināt
  • Formāts: 272 pages
  • Izdošanas datums: 18-Jun-2020
  • Izdevniecība: Oxford University Press
  • Valoda: eng
  • ISBN-13: 9780192607041
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This accessible primer has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics.

A Primer of Population Genetics and Genomics has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics.

Recent textbooks have tended to focus on such specialized topics as the coalescent, molecular evolution, human population genetics, or genomics. This primer bucks that trend by encouraging a broader familiarity with, and understanding of, population genetics and genomics as a whole. The overview ranges from mating systems through the causes of evolution, molecular population genetics, and the genomics of complex traits. Interwoven are discussions of ancient DNA, gene drive, landscape genetics, identifying risk factors for complex diseases, the genomics of adaptation and speciation, and other active areas of current research. The principles are illuminated by numerous examples from a wide variety of animals, plants, microbes, and human populations. The approach also emphasizes learning by doing, which in this case means solving numerical or conceptual problems. The rationale behind this is that the use of concepts in problem-solving lead to deeper understanding and longer knowledge retention.

This accessible, introductory textbook is aimed principally at students of various levels and abilities (from senior undergraduate to postgraduate) as well as practising scientists in the fields of population genetics, ecology, evolutionary biology, computational biology, bioinformatics, biostatistics, physics, and mathematics.
1 Genetic Polymorphisms
1(20)
1.1 Genetic and Molecular Background
2(3)
Genotype and Phenotype
2(1)
Gene Expression
2(3)
1.2 Major Types of Polymorphisms
5(3)
DNA Polymorphisms
5(2)
Utility of DNA Polymorphisms
7(1)
1.3 Allele and Genotype Frequencies
8(3)
1.4 Populations and Models
11(10)
Models
11(2)
Utility of Mathematical Models
13(1)
Discrete-Time Models
13(2)
Continuous-Time Models
15(1)
How Models are Tweaked
16(5)
2 Organization of Genetic Variation
21(26)
2.1 Random Mating
21(10)
The Hardy--Weinberg Principle
22(1)
Constancy of Allele Frequencies
23(1)
Chi-square Test for Hardy--Weinberg Equilibrium
24(2)
Statistical Power of the Chi-square Test for Hardy--Weinberg Equilibrium
26(2)
Recessive Alleles Hidden in Heterozygotes
28(1)
Multiple Alleles and DNA Typing
29(2)
2.2 X-Linked Genes
31(2)
2.3 Multiple Loci: Linkage and Linkage Disequilibrium
33(5)
Linkage Disequilibrium, Genetic Associations, and the Problem of Multiple Comparisons
37(1)
2.4 Linkage Disequilibrium in Natural Populations
38(9)
Linkage Disequilibrium as a Correlation Between Alleles of Different Genes in Gametes
39(2)
Linkage Disequilibrium Due to Population Admixture
41(1)
Wahlund's Principle
42(5)
3 Inbreeding and Population Structure
47(28)
3.1 Genotype Frequencies with Inbreeding
47(2)
3.2 The Inbreeding Coefficient
49(5)
Inbreeding Depression and Heterosis
51(1)
Effects of Inbreeding on Rare Harmful Alleles
52(1)
Inbreeding Effects in Human Populations
53(1)
3.3 Calculation of the Inbreeding Coefficient from Pedigrees
54(3)
3.4 Regular Systems of Mating
57(5)
Partial Selfing
58(1)
Repeated Sib Mating
59(2)
Recombinant Inbred Lines
61(1)
3.5 Remote Inbreeding in Finite Populations
62(13)
Identity by Descent in Finite Populations
63(2)
Decreased Heterozygosity in Admixed Populations
65(3)
Hierarchical Population Structure
68(2)
Mating Between Relatives in a Structured Population
70(5)
4 Mutation, Gene Conversion, and Migration
75(34)
4.1 Mutation
75(7)
Irreversible Mutation
76(1)
Reversible Mutation
77(1)
Gene Duplication and Functional Divergence
78(3)
Equilibrium Heterozygosity with Mutation
81(1)
4.2 The Coalescent
82(12)
Coalescence in the Wright--Fisher Model
83(2)
Nucleotide Polymorphism
85(1)
Nucleotide Diversity
86(1)
Estimating θ and π from Sequence Data
86(2)
The Moran Model
88(2)
Effective Population Number
90(4)
4.3 Gene Conversion
94(3)
Biased Gene Conversion
94(1)
A Model of Biased Gene Conversion
95(2)
4.4 Migration
97(12)
Models of Migration
97(1)
One-Way Migration
98(1)
The Island Model of Migration
98(1)
How Migration Limits Genetic Divergence
99(2)
The Fixation Index FST in Relation to Coalescence
101(2)
Stepping-Stone Models
103(6)
5 Natural Selection in Large Populations
109(38)
5.1 Selection in Haploids
109(3)
Continuous-Time Model of Haploid Selection
109(2)
Discrete-Generation Model of Haploid Selection
111(1)
5.2 Selection in Diploids
112(14)
Directional Selection
112(3)
Time Required for Changes in Allele Frequency
115(2)
Selective Sweeps: Hard Sweeps and Soft Sweeps
117(1)
Probability of Survival of a Favorable Mutation
118(3)
Overdominance and Heterozygote Inferiority
121(4)
Evolutionary Change in Fitness
125(1)
5.3 Mutation--Selection Balance
126(6)
Equilibrium Allele Frequencies for Recessive and Partially Dominant Mutations
127(1)
Degree of Dominance of Severely Versus Mildly Deleterious Mutations
128(1)
Background Selection
129(2)
Balance Between Migration and Selection
131(1)
5.4 Gametic Selection and Meiotic Drive
132(5)
Gametic Selection
133(1)
Meiotic Drive
134(1)
Gene Drive
135(2)
5.5 Other Modes of Selection
137(10)
6 Random Genetic Drift in Small Populations
147(32)
6.1 Differentiation of Subpopulations Under Random Drift
147(8)
Random Drift in Small Experimental Populations
148(1)
The Probability Process Underlying the Wright--Fisher Model
149(2)
Transition Matrix for the Moran Model
151(1)
Change in Average Allele Frequency Among Subpopulations
152(2)
Decrease in Average Heterozygosity Among Subpopulations
154(1)
6.2 Diffusion Approximations
155(4)
The Forward Equation: An Approach Looking Forward in Time
156(3)
The Backward Equation: Musing on the First Step
159(1)
6.3 Fixation Probabilities and Times to Fixation
159(5)
Probability of Fixation
160(2)
Times to Fixation or Loss
162(2)
6.4 Equilibrium Distributions of Allele Frequency
164(15)
An Equation for the Stationary Distribution
164(1)
Reversible Mutation
165(2)
Multiple Alleles and the Ewens Sampling Formula
167(2)
Migration
169(1)
Mutation-Selection Balance
170(1)
Protein Polymorphisms
171(8)
7 Molecular Population Genetics
179(46)
7.1 Rates of Nucleotide Substitution
180(9)
Nucleotide Substitutions in Noncoding DNA
180(2)
Synonymous and Nonsynonymous Substitutions
182(1)
Nucleotide Divergence Between Species
182(2)
Correction for Multiple Mutational Hits
184(2)
Amino Acid Divergence Between Species
186(1)
Molecular Clockwork
187(2)
7.2 Analysis of the Site Frequency Spectrum
189(8)
The Unfolded Site Frequency Spectrum
189(4)
The Folded Site Frequency Spectrum
193(1)
Codon Usage Bias
194(1)
Selection for Optimal Codons and Amino Acids
195(2)
7.3 Polymorphism and Divergence
197(9)
The McDonald--Kreitman Test
197(3)
Refinements of the McDonald--Kreitman Test
200(1)
Polymorphism and Divergence as a Poisson Random Field
201(3)
The Hudson--Kreitman--Aguade Test
204(1)
Neutrality Versus Selection: An Emerging Consensus
205(1)
7.4 Demographic History
206(3)
Changes in Population Size Through Time
206(1)
Population Splits and Fusions
207(1)
Estimating Parameters in Demographic Models
208(1)
7.5 Ancient DNA in Studies of Human Populations
209(4)
Human Origins
209(1)
Technical Challenges of Ancient DNA
210(1)
Insights into Human History from Ancient DNA
210(3)
7.6 Transposable Elements
213(12)
Insertion Sequences and Transposons in Bacteria
214(1)
Transposable Elements in Eukaryotes
215(10)
8 Population Genetics of Complex Traits
225(38)
8.1 Phenotypic Variation in Complex Traits
225(4)
Three Types of Complex Traits
226(1)
Phenotypic Variation
226(1)
Properties of the Normal Distribution
227(2)
8.2 Genes and Environment
229(9)
Genotypic Variance and Environmental Variance
230(1)
Broad-Sense Heritability
231(1)
Genotype-by-Environment and Other Interactions
232(1)
Genetic Effects on Complex Traits
233(1)
Components of Genotypic Variation
234(2)
Physiological Epistasis Versus Statistical Epistasis
236(2)
8.3 Artificial Selection
238(11)
Prediction Equation for Individual Selection
240(2)
Intensity of Selection
242(1)
Genetic Basis of the Prediction Equation
243(2)
Change in Mean Phenotype from One Generation of Selection
245(1)
Effect of Selection on a Constituent Locus of a Complex Trait
246(1)
Genomic Selection
247(1)
Correlated Response to Selection
248(1)
8.4 Resemblance Between Relatives
249(4)
Parent--Offspring Covariance
249(1)
Covariance Between Relatives
250(1)
Heritability Estimates from Covariance
251(1)
Heritability Estimates from Regression
251(2)
8.5 Complex Traits with Discrete Expression
253(10)
Threshold Traits: Genes as Risk Factors
253(1)
Heritability of Liability
253(3)
Applications to Human Disease
256(7)
9 Complex Traits in Natural Populations
263(28)
9.1 Genetic Variation and Phenotypic Evolution
263(6)
Mutational Variance and Standing Variance
264(1)
Phenotypic Evolution Under Directional Selection
265(2)
Phenotypic Evolution Under Stabilizing Selection
267(2)
9.2 Searching for the Genes Affecting Complex Traits
269(9)
Quantitative Trait Loci
269(3)
Candidate Genes
272(2)
Genome-Wide Association Studies
274(1)
Number of Genes and Magnitude of Effects
275(2)
Genetic and Environmental Risk Factors in Complex Traits
277(1)
9.3 Complex Traits in Evolutionary Adaptation
278(3)
Evolutionary Pathways of Drug Resistance
279(1)
Genomic Changes Under Domestication
280(1)
Local Selection Versus Gene Flow
281(1)
9.4 Complex Traits in Speciation
281(10)
Reinforcement of Mating Barriers
282(1)
Reproducibility of Phenotypic and Genetic Changes in Speciation
282(1)
Accumulation of Genetic Incompatibilities
283(8)
Index 291
Daniel L. Hartl is Higgins Professor of Biology in the Department of Organismic and Evolutionary Biology at Harvard University. His laboratory studies population genetics and genomics as well as molecular evolution. He has been awarded the Thomas Hunt Morgan Medal of the Genetics Society of America and is an elected member of the National Academy of Sciences USA as well as the American Academy of Arts and Sciences. His PhD is from the University of Wisconsin, and he did postdoctoral studies at the University of California, Berkeley. He has served on the faculties of the University of Minnesota, Purdue University, and Washington University Medical School in St. Louis. In addition to 450 scientific articles, Hartl has authored or coauthored 35 books.
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