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E-grāmata: Primer of Molecular Population Genetics

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(Professor, Department of Ecology & Evolutionary Biology, University of Toronto, Canada)
  • Formāts: 304 pages
  • Izdošanas datums: 06-Jun-2019
  • Izdevniecība: Oxford University Press
  • Valoda: eng
  • ISBN-13: 9780192575548
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Primer of Molecular Population GeneticsPalielināt
  • Formāts: 304 pages
  • Izdošanas datums: 06-Jun-2019
  • Izdevniecība: Oxford University Press
  • Valoda: eng
  • ISBN-13: 9780192575548
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What are the genomic signatures of adaptations in DNA? How often does natural selection dictate changes to DNA? How does the ebb and flow in the abundance of individuals over time get marked onto chromosomes to record genetic history? Molecular population genetics seeks to answer such questions by explaining genetic variation and molecular evolution from micro-evolutionary principles. It provides a way to learn about how evolution works and how it shapes species by incorporating molecular details of DNA as the heritable material. It enables us to understand the logic of how mutations originate, change in abundance in populations, and become fixed as DNA sequence divergence between species. With the revolutionary advances in genomic data acquisition, understanding molecular population genetics is now a fundamental requirement for today's life scientists. These concepts apply in analysis of personal genomics, genome-wide association studies, landscape and conservation genetics, forensics, molecular anthropology, and selection scans. This book introduces, in an accessible way, the bare essentials of the theory and practice of molecular population genetics.

Recenzijas

This is a timely and interesting book that will not quickly become outdated and that will attract many scientists to the fascinating field of molecular genetics as it applies to questions of ecological relevance. * Conservation Biology *

1 Introduction: What is molecular population genetics?
1(10)
1.1 On the origins of molecular population genetics
1(7)
1.2 What is the use of molecular population genetics?
8(3)
Further reading
10(1)
2 The origins of molecular diversity
11(23)
2.1 Kinds of mutations
11(11)
2.1.1 Single nucleotide mutation
11(7)
2.1.2 Simple insertions and deletions
18(1)
2.1.3 Tandem repeat mutations
18(2)
2.1.4 Transposable elements
20(1)
2.1.5 Duplications and large-scale mutations
21(1)
2.2 Fitness effects of new mutations
22(5)
2.2.1 Deleterious mutations
22(3)
2.2.2 Neutral and nearly neutral mutations
25(1)
2.2.3 Advantageous mutations
26(1)
2.2.4 Magnitude and distribution of effects
26(1)
2.3 Models of mutation
27(7)
2.3.1 Recurrent mutation model
28(1)
2.3.2 Infinite alleles model
29(1)
2.3.3 Infinite sites model
29(1)
2.3.4 Finite sites models
29(1)
2.3.5 Stepwise mutation model
30(1)
2.3.6 Birth-death model of gene duplication
30(1)
2.3.7 Biological complexities in mutation
31(1)
Further reading
32(2)
3 Quantifying genetic variation at the molecular level
34(33)
3.1 Heterozygosity
36(6)
3.2 Allozyme variation
42(1)
3.3 DNA sequence variation
43(9)
3.3.1 Nucleotide polymorphism and diversity: θw and θπ
44(6)
3.3.2 The site frequency spectrum
50(2)
3.4 Simple sequence repeat variation
52(1)
3.5 Other measures of molecular diversity
52(2)
3.6 Genetic variation among multiple populations
54(13)
3.6.1 Quantifying population genetic structure with FST
54(5)
3.6.2 Migration models and effects on population subdivision
59(6)
Further reading
65(2)
4 Neutral theories of molecular evolution
67(18)
4.1 The standard neutral model
67(11)
4.1.1 Neutral divergence and the molecular clock
69(5)
4.1.2 Neutral predictions for polymorphism
74(4)
4.2 Nearly Neutral Theory
78(3)
4.3 More complex models of selective neutrality
81(1)
4.4 Misconceptions about Neutral Theory
82(3)
Further reading
83(2)
5 Genealogy in evolution
85(28)
5.1 Gene trees forward-in-time within species
85(3)
5.2 Gene trees in reverse-time coalescence within species
88(6)
5.3 Gene trees, species trees, and phylogeny among species
94(16)
5.3.1 Substitution rates in divergence
98(6)
5.3.2 Multiple hits in sequence divergence
104(3)
5.3.3 Phylogeny: topology, discordance, and molecular clocks
107(3)
5.4 Effects of recombination and hybridization on genealogies
110(3)
Further reading
112(1)
6 Recombination and linkage disequilibrium in evolutionary signatures
113(16)
6.1 Linkage disequilibrium: what is it?
115(1)
6.2 The causes of linkage disequilibrium
116(3)
6.3 Measuring linkage disequilibrium
119(7)
6.4 Gene conversion: non-crossover recombination
126(3)
Further reading
128(1)
7 Natural selection and demography as causes of molecular non-randomness
129(30)
7.1 Natural selection
129(14)
7.1.1 Positive selection
130(6)
7.1.2 Balancing selection
136(2)
7.1.3 Purifying selection
138(4)
7.1.4 Connecting notions of selection at phenotypic and molecular levels
142(1)
7.2 Population size changes
143(3)
7.2.1 Population expansions
144(1)
7.2.2 Population contractions and bottlenecks
145(1)
7.3 Population structure and migration
146(7)
7.3.1 Population structure and genealogies
148(5)
7.3.2 Local adaptation in subpopulations
153(1)
7.4 Genomic compartments of chromosomal linkage
153(6)
Further reading
158(1)
8 Molecular deviants: Sequence signatures of selection and demography
159(36)
8.1 Skewed patterns of polymorphism
159(11)
8.1.1 Too little or too much polymorphism
161(3)
8.1.2 Skewed site frequency spectra
164(6)
8.2 Sequence divergence and differentiation
170(11)
8.2.1 KA/KS ratios
171(4)
8.2.2 Population differentiation and Fst outliers
175(5)
8.2.3 Characterizing population structure and admixture
180(1)
8.3 Polymorphism and divergence
181(10)
8.3.1 The HKA test
182(2)
8.3.2 The MK test
184(5)
8.3.3 Extensions to the "MK framework"
189(2)
8.4 Connecting quantitative genetics and molecular population genetics
191(4)
Further reading
192(3)
9 Case studies in molecular population genetics: Genotype to phenotype to selection
195(22)
9.1 Coat color adaptation in mice
195(5)
9.2 Flight ability in butterflies
200(2)
9.3 Insecticide resistance in Drosophila
202(3)
9.4 Body armor in stickleback fish
205(4)
9.5 Alcohol tolerance in Drosophila
209(3)
9.6 Advanced issues in molecular evolutionary signatures
212(5)
Further reading
214(3)
Glossary of units, metrics, acronyms, and abbreviations 217(6)
Glossary of terms and jargon 223(20)
Index 243
Asher D. Cutter is a Professor in the Department of Ecology & Evolutionary Biology at the University of Toronto. He earned a B.S. in Biology and Environmental Studies at Tufts University and was awarded a Fulbright Scholarship for post-graduate study in Australia at James Cook University. After completing a Ph.D. in Ecology and Evolutionary Biology at the University of Arizona, he studied as a post-doctoral fellow at the University of Edinburgh as an NSF International Scholar. While at the University of Toronto, he has served as Canada Research Chair in Evolutionary Genomics and as Associate Chair for Undergraduate Studies.
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