Genetic Distance (FST)

Before you can model your ancestry in detail, you need a starting point. FST is the fastest way to find one.

What FST measures

FST is a single number between 0 and 1 that measures how genetically distant two populations are. The bigger the number, the more they've drifted apart over time.

For rough orientation: two populations from the same village might have an FST around 0.001, almost no difference. Modern Europeans compared to modern East Asians come in around 0.07. Modern Europeans compared to populations from sub-Saharan Africa: roughly 0.15.

When to use it

On IoA, FST is the scouting tool. You compare your DNA against every reference population in the AADR and see which ones come up closest. Those closest matches are usually the right starting points for a qpAdm run later.

Most users run a genetic distance scan first, then use the results to pick sources for admixture analysis.

Pseudohaploid

Most ancient samples in AADR are stored as pseudohaploid. That's a technical detail with practical consequences: at each genome position, the database only records one allele instead of both, because the original sequencing reads were too sparse to confidently call both.

Modern samples like your raw DNA file are diploid. Both alleles at each position are known.

When you compare a diploid modern sample directly against pseudohaploid ancient samples, this asymmetry introduces a small bias in the FST values. The Adjust pseudohaploid option corrects for it.