PCA and ancestry: real PCA on simulated genotypes

Populations

Individuals per population

Markers

More markers, tighter clusters. Structure is a property of the aggregate.

Fst between populations

Logarithmic slider. About 0.005 between neighbouring European countries, 0.10 to 0.15 between continents.

Structure

Stepping stone makes each population a neighbour of the last, so distance in the plot is distance along a line.

Ascertainment

Genotyping arrays carry markers picked for being variable in whoever was sequenced first.

Admixed individuals

Each allele copy comes from population 1 with probability alpha and from population 2 otherwise.

Admixture proportions

Real admixture is correlated along the chromosome, in blocks that the recombination tool's Generations tab draws. Drawing each marker independently gets the PCA position right and the block structure wrong, which is adequate for the PCA and not for local ancestry inference.

Seed

PCA

Individuals-

Markers used-

PC1 variance-

PC2 variance-

Estimated Fst-

PCA

The same thing in R Copy

The same thing in R