Statistical Genetics and Genomics

2.

Population Genetics Principles

2.1.

Genetic Variation in Populations

2.1.1.

Allele Frequencies

2.1.1.1.

Calculation Methods

2.1.1.2.

Sampling Effects

2.1.1.3.

Minor Allele Frequency

2.1.2.

Genotype Frequencies

2.1.2.1.

Observed vs Expected Frequencies

2.1.2.2.

Hardy-Weinberg Calculations

2.1.3.

Measures of Genetic Diversity

2.1.3.1.

2.1.3.2.

Nucleotide Diversity

2.1.3.3.

Allelic Richness

2.1.3.4.

Shannon Diversity Index

2.2.

Hardy-Weinberg Equilibrium

2.2.1.

Fundamental Assumptions

2.2.1.1.

2.2.1.2.

2.2.1.3.

2.2.1.4.

2.2.1.5.

Infinite Population Size

2.2.2.

Hardy-Weinberg Calculations

2.2.2.1.

Two-Allele Systems

2.2.2.2.

Multiple-Allele Systems

2.2.2.3.

Sex-linked Loci

2.2.3.

Testing for Hardy-Weinberg Equilibrium

2.2.3.1.

Chi-squared Test

2.2.3.2.

2.2.3.3.

Interpreting Deviations

2.3.

Evolutionary Forces

2.3.1.

2.3.1.1.

Mutation Rates and Patterns

2.3.1.2.

Mutation-Selection Balance

2.3.1.3.

Neutral Mutations

2.3.2.

Natural Selection

2.3.2.1.

Fitness and Selection Coefficients

2.3.2.2.

Directional Selection

2.3.2.3.

Balancing Selection

2.3.2.4.

Frequency-Dependent Selection

2.3.2.5.

Selection at Multiple Loci

2.3.3.

2.3.3.1.

Random Sampling Effects

2.3.3.2.

Effective Population Size

2.3.3.3.

Bottlenecks and Founder Effects

2.3.3.4.

Fixation Probability

2.3.4.

2.3.4.1.

Migration Models

2.3.4.2.

2.3.4.3.

Stepping-Stone Model

2.3.4.4.

Effects on Population Differentiation

2.3.5.

Non-Random Mating

2.3.5.1.

2.3.5.2.

Assortative Mating

2.3.5.3.

Population Subdivision

2.3.5.4.

2.4.

Linkage and Recombination

2.4.1.

Principles of Genetic Linkage

2.4.1.1.

Recombination Frequency

2.4.1.2.

Genetic Distance

2.4.1.3.

Physical vs Genetic Distance

2.4.2.

Linkage Disequilibrium

2.4.2.1.

Definition and Measurement

2.4.2.2.

D and D' Statistics

2.4.2.3.

Correlation Coefficient r²

2.4.2.4.

Factors Affecting LD

2.4.3.

Haplotype Structure

2.4.3.1.

Haplotype Definition

2.4.3.2.

Haplotype Blocks

2.4.3.3.

Recombination Hotspots

2.4.3.4.

Haplotype Diversity

2.5.

Population Structure and Demography

2.5.1.

Population Differentiation

2.5.1.1.

2.5.1.2.

Fst Calculation and Interpretation

2.5.1.3.

Hierarchical F-statistics

2.5.2.

Population Stratification

2.5.2.1.

Causes and Consequences

2.5.2.2.

Detection Methods

2.5.2.3.

Principal Component Analysis

2.5.2.4.

Multidimensional Scaling

2.5.3.

Admixture Analysis

2.5.3.1.

Admixture Models

2.5.3.2.

Ancestry Proportions

2.5.3.3.

Local Ancestry Inference

2.5.3.4.

Admixture Mapping

2.5.4.

Demographic History

2.5.4.1.

Population Bottlenecks

2.5.4.2.

Population Expansions

2.5.4.3.

Migration Patterns

2.5.4.4.

Coalescent Theory

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