My genome among ancient populations

In my previous post, Am I 100% Republican Roman?, I examined a result that seemed to offer a remarkably simple answer to my ancestry: a model could describe my genome using only a reference group labelled Republican Rome.

That leaves a different question: where does my genome sit when we compare it directly with ancient individuals from different places and periods? Here I explore that question visually, using two ancient-DNA PCA comparisons. I ask which affinities recur—and how much the picture changes when modern rather than ancient people define the axes.

This also extends the visual approach in my earlier post, Painting Geographic Maps with DNA, and the accompanying PCA Atlas. Those geographic maps described variation among people living today; this comparison turns to people who lived in the past.

Two ways to draw the genetic map

Principal component analysis compresses genetic variation into a few axes. Nearby points have similar scores on the dimensions shown. These are genetic plots, not geographic maps: moving left or right does not translate directly into travelling west or east.

In the first analysis, 269 modern individuals define the axes. Ancient genomes and my own genome are then placed onto that fixed reference frame. In the second, 44 high-call-rate ancient individuals define a separate frame, and the remaining genomes are placed onto it. My genome is held out of both fits, so it does not determine either set of axes.

Both analyses use the same 76,159 SNPs. This matters because it holds the marker set constant while changing the people who define the axes. The two panels are independently centred and scaled; their PC1 and PC2 coordinates are not interchangeable. This modern-reference comparison is also a separate analysis from the existing Europe-wide atlas PCA.

Below, I examine which ancient populations fall closest to my genome—and why the answer changes with the reference panel.