Population Genetics

Genetic variation in populations and the forces that change it: measuring variation, Hardy–Weinberg and the EM algorithm, single-locus selection, drift and effective population size, Kimura’s fixation theory, the coalescent and Tajima’s D, F-statistics, gene flow and admixture, linkage disequilibrium and selective sweeps, detecting selection in genomes, and quantitative genetics, QTL and GWAS, ending in a capstone on genetic rescue, forensic match probabilities with Canada’s National DNA Data Bank and CODIS, and Indigenous data governance through the CARE principles and Silent Genomes.

BIOL-322 Year 3 3 credits 12 lessons · 5 h 34 min

Offered by HSM University · Biology

This is the Canadian version of this course. See the American version.

What you'll learn

Describe the main classes of genetic variation, estimate allele frequencies, heterozygosity and nucleotide diversity with measures of uncertainty, and compute and interpret the site frequency spectrum.
Apply Hardy–Weinberg principles to multiple-allele and X-linked loci, estimate hidden allele frequencies with the EM algorithm, and test genotype proportions with the exact test.
Analyse single-locus selection models, find equilibria and assess their stability, calculate times to fixation and predict mutation–selection balance.
Model genetic drift as a stochastic process, compute exact absorption probabilities and times, and estimate effective population size from demographic and genetic data.
Use Kimura’s fixation probability to determine when selection or drift dominates, explain nearly neutral theory and the drift barrier, and calculate mutation–drift equilibria.
Explain coalescent theory, calculate Watterson’s θ, nucleotide diversity and Tajima’s D, and interpret them in light of demographic history and selection.
Partition population structure with F-statistics, recognize the Wahlund effect, estimate F_ST appropriately and relate it to coalescence times and the island model.
Measure gene flow directly and indirectly, test isolation by distance, estimate and date admixture, and interpret PCA and clustering results responsibly.
Calculate D, D′ and r², explain how recombination and drift set levels of linkage disequilibrium, and identify the genomic signatures of sweeps and background selection.
Detect selection with dN/dS, the McDonald–Kreitman test, the population branch statistic and related methods, and evaluate the evidence needed to establish adaptation.
Relate quantitative genetic variance to allele frequencies and effects, explain QTL mapping and GWAS including correction for stratification, and evaluate the portability and limits of polygenic scores without essentialist reasoning about ancestry.
Apply population genetics to genetic rescue, forensic match probabilities and founder-effect disease screening in Canadian and international contexts, and explain Indigenous data governance through the CARE principles and Silent Genomes.

Course content

12 lessons · 5 h 34 min total · final exam

1 Genetic variation and its measurement 30 min · quiz
2 Hardy–Weinberg, multiple alleles and estimating allele frequencies 32 min · quiz
3 Natural selection: single-locus models and equilibria 29 min · quiz
4 Genetic drift and effective population size 28 min · quiz
5 The interplay of drift, selection and mutation 26 min · quiz
6 The coalescent and neutral diversity statistics 26 min · quiz
7 Population structure and F-statistics 26 min · quiz
8 Gene flow, isolation by distance and admixture 27 min · quiz
9 Linkage disequilibrium, recombination and selective sweeps 26 min · quiz
10 Detecting selection in molecular data 27 min · quiz
11 Quantitative genetics, QTL and GWAS 26 min · quiz
12 Capstone: population genetics in conservation, forensics and human health 31 min · quiz
E Final exam 20 questions

Requirements

Recommended background. You can start any course at any time.

Description

Part of the Science stream, typically taken in year 3.