Population Genetics

9.

Molecular Population Genetics

9.1.

Molecular Markers

9.1.1.

Types of Markers

9.1.1.1.

9.1.1.2.

9.1.1.3.

Microsatellites

9.1.1.4.

9.1.1.5.

Mitochondrial DNA

9.1.1.6.

Chloroplast DNA

9.1.2.

Marker Properties

9.1.2.1.

Inheritance Patterns

9.1.2.2.

9.1.2.3.

Level of Polymorphism

9.2.

DNA Sequence Analysis

9.2.1.

Sequence Alignment

9.2.2.

Polymorphism Detection

9.2.3.

Phylogenetic Relationships

9.3.

9.3.1.

Kimura's Neutral Theory

9.3.2.

Nearly Neutral Theory

9.3.3.

9.3.3.1.

Molecular Clock

9.3.3.2.

Polymorphism Patterns

9.3.3.3.

Substitution Rates

9.4.

Tests of Neutrality

9.4.1.

9.4.2.

Fu and Li's Tests

9.4.3.

McDonald-Kreitman Test

9.4.4.

9.5.

Detecting Selection

9.5.1.

Synonymous vs Non-synonymous Sites

9.5.2.

9.5.3.

Codon Usage Bias

9.5.4.

Linkage Disequilibrium Patterns

9.6.

Population History Inference

9.6.1.

Coalescent Theory

9.6.2.

Demographic Inference

9.6.3.

Migration Patterns

9.6.4.

Population Bottlenecks

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8. Mating Systems and Population Structure

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10. Quantitative Genetics