Notebook for HG
Preface
1
An Introduction to human genetics
1.1
Some very useful numbers for human population genetics
1.2
A genome owner’s starter pack
1.3
Human genome variation and why it matters
1.4
DNA sequencing: a fundamental tool for studying biology
1.5
Mutation: The ultimate source of genetic variation
2
Population genetics: the forces that shape genetic variation
2.1
Genetic Drift: What happens to alleles over time?
2.1.1
The Wright-Fisher (WF) model of genetic drift
2.1.2
Binomial sampling over successive generations produces genetic drift
2.1.3
mutation and drift
2.1.4
mutation, drift and the amount of genetic variation
2.1.5
effective population size
2.1.6
the WF model with haplotypes
2.1.7
WF simulation of haplotype variation
2.2
More on genetic drift: The coalescent
2.2.1
A short history
2.2.2
Inheritance of genetic material from a shared ancestor
2.2.3
The coalescent refers to ancient shared ancestry within populations
2.2.4
Time to coalescence
2.2.5
Understanding waiting-time distributions: the geometric distribution
2.2.6
Understanding waiting-time distributions: the exponential distribution
2.2.7
The time distribution for two samples
2.2.8
The coalescent for larger samples
2.2.9
Coalescent with mutation
2.2.10
Quantitative aspects of variation in the coalescent
2.2.11
The coalescent with population size changes
2.2.12
The coalescent and the fixation process
2.2.13
Coalescent simulation of haplotype variation
2.3
Linkage, recombination, and LD
2.3.1
A first look at haplotype structure
2.3.2
Linkage generates haplotype structure (or equivalently, LD)
2.3.3
Recombination
2.3.4
Measuring LD between pairs of SNPs
2.3.5
Strong recombination breaks down LD
2.3.6
The coalescent with recombination: the ARG
2.3.7
Recombination and LD in human data
2.3.8
PRDM9 and the hotspot paradox
2.3.9
Haplotype copying models
2.4
Genetic drift in structured populations
2.4.1
Humans share a recent African origin
2.4.2
Allele freqeuncy variation across populations
2.4.3
Models of population separation and drift
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1
An Introduction to human genetics
1.1
Some very useful numbers for human population genetics
1.2
A genome owner’s starter pack
1.3
Human genome variation and why it matters
1.4
DNA sequencing: a fundamental tool for studying biology
1.5
Mutation: The ultimate source of genetic variation