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. 2024 Jan 30;13:e79714. doi: 10.7554/eLife.79714

Figure 2. Armenia: two homogeneous genetic clusters distinguished by a temporal shift.

(A) Sampling locations of ancient genomes (open circles) colored by their genetic cluster identified using qpAdm modeling. (B) Date ranges for the genomes: each line represents the 95% confidence interval for the radiocarbon date or the upper and lower limit of the inferred date, and the point represents the midpoint of that range. (C) Projections of the genomes onto a PCA of present-day genomes (gray points labeled by their population). Present-day genomes from Armenia are shown with dark gray open circles.

Figure 2.

Figure 2—figure supplement 1. Principal component analysis of present-day genomes from Europe and the Mediterranean.

Figure 2—figure supplement 1.

PCA was performed on 829 individuals (480,712 snps) using smartpca v1600. The following parameters were used: 5 outlier iterations (numoutlieriter), 10 principal components along which to remove outliers (numoutlierevec), altnormstyle set to NO, with least squares projection turned on (lsqproject set to YES).
Figure 2—figure supplement 2. Ancestry clusters identified within regions.

Figure 2—figure supplement 2.

Each row displays data from a single study region. The first column shows a map with the sampling locations for the individuals, while columns two through four show the individuals projected onto a PCA space of present-day genomes (gray points) (populations are labeled in the far right panel in row 1 and in Figure 2—figure supplement 1). Individual ancient genomes in the map and PCA panels are colored by ancestry clusters identified using qpAdm. Colors are not matched across regions. Star points are putative outliers, that is individuals with ancestry that is underrepresented in the region. They are not colored by ancestry clusters so as to reduce visual clutter.
Figure 2—figure supplement 3. SNP coverage comparison across cluster sizes and downstream outlier status.

Figure 2—figure supplement 3.

(left) No significant correlation was detected between the median number of SNPs covered across the individuals in a cluster and cluster size. (right) There also was no significant difference in the number of SNPs covered between outlier and non-outlier clusters.