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Population Genetics and Evolutionary Processes

Manual: General · Subject: Genetics

Develop formal tools to connect allele frequency change, drift, selection, migration, recombination, and demographic history.

Population genetics as the bridge between mechanism and history

Forces acting on allele frequencies

Allele frequencies change through natural selection, genetic drift, mutation, migration, and recombination. Population structure and demography can mimic selection, making careful modeling essential for interpretation.

Important population-genetic quantities

Allele frequency
The proportion of copies of an allele in a population.
Effective population size
An idealized size capturing the strength of drift relative to a real population.
Fixation
The process by which an allele reaches frequency 11.
Selective sweep
A rapid rise in frequency of a favored allele and linked haplotype.
FST
A summary of genetic differentiation among populations.

The Hardy-Weinberg baseline

Under random mating, no selection, no migration, no mutation, and infinite population size, genotype frequencies follow p2p^2, 2pq2pq, and q2q^2. Deviations from this baseline often reveal biologically important processes, but they are not by themselves proof of selection.

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Interpretation discipline

The same frequency pattern can arise from selection, bottlenecks, relatedness, or population substructure. Population genetics is inference under confounding, not a simple checklist.

Drift versus selection

Genetic drift

  • Random sampling effect
  • Stronger in small populations
  • Can fix neutral or mildly deleterious alleles

Natural selection

  • Non-random frequency change tied to fitness
  • Can be positive, negative, or balancing
  • Often leaves genomic signatures such as reduced diversity or haplotype structure

In the Hardy-Weinberg model, if p=0.7p = 0.7 for one allele, what is the expected heterozygote frequency?

What is an effective population size, and why is it often smaller than census size?

How to infer selection from genomic data

  1. 1

    Estimate baseline demography from neutral or near-neutral sites.

  2. 2

    Test whether candidate loci show excess differentiation, long haplotypes, or skewed allele frequency spectra.

  3. 3

    Control for recombination rate, background selection, and structure.

  4. 4

    Validate the functional consequence of the candidate variant or haplotype.

A bottleneck most directly increases the effect of: