Population Genomics in Practice 2025
  • Slides
  • Exercises
  • Code recipes
  1. Slides
  2. Population genetics foundations
  3. Listing
  • Slides
    • Listing
    • Introduction
      • Population genomics in practice
    • Population genetics foundations
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      • Data and definitions
      • Alleles and genealogies
      • Linkage disequilibrium
      • The Wright-Fisher model
      • Genetic diversity
      • Selection
    • Variant calling
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      • DNA sequencing data
      • Read mapping
      • Variant calling and genotyping
      • Variant calling workflows
    • Variant filtering
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      • Variant filtering
      • Depth filtering
    • Genetic diversity
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      • Genetic diversity
    • Population structure
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      • Principal component analysis
      • Admixture
    • Demography
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    • Selection
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    • Simulation
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      • Brief introduction to simulation packages and stdpopsim
      • Primer on the coalescent and forward simulation
      • Ancestral recombination graph inference
  • Exercises
    • Listing
    • Data
      • Compute environment
      • Monkeyflowers dataset
    • Variant calling
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      • Variant calling introduction
      • Data quality control
      • Read mapping and duplicate removal
      • Variant calling workflow
    • Variant filtering
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      • Basic variant filtering
      • Depth filtering on invariant sites
    • Recombination and linkage
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      • Linkage disequilibrium decay
    • Genetic diversity
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      • Genetic diversity landscapes
    • Population structure
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      • Principal component analysis
      • Admixture
      • D-statistics
    • Simulation
      • Listing
      • HOWTO
      • Introduction to stdpopsim
      • Simulating selection with stdpopsim
      • Introduction to simulation with msprime
  • Code recipes
    • Code recipes

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  • About
  • Listing
  1. Slides
  2. Population genetics foundations
  3. Listing

Population genetics foundations

Collection of short presentations on population genetic theory and foundations
Published

18-Sep-2025

About

Collection of short presentations on population genetic theory and foundations

Listing

Title Description
Data and definitions Introduction to population genetic data and definitions.
Alleles and genealogies Introduction to alleles and genealogies
Linkage disequilibrium Basic introduction to linkage disequilibrium and recombination. Based on Pritchard (n.d.)
The Wright-Fisher model Introduction to the Wright-Fisher population model and relationship to genealogies
Genetic diversity Genetic drift, effective population size and the evolution of genetic diversity
Selection Overview of natural selection
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References

Pritchard, J. K. (n.d.). An Owner’s Guide to the Human Genome. Retrieved August 18, 2025, from https://web.stanford.edu/group/pritchardlab/HGbook.html

2025 NBIS | GPL-3 License

 

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