Armenians’ relationship to world populations

To study the Armenians’ genetic relationship to worldwide populations, we computed principal components using 78 populations (Supplementary Table 1) and projected the Armenians onto the plot in a procedure called ‘PCA projection’14 (Figure 2a), which ensures that the PCA patterns are not affected by the large number of Armenians used in the analysis. We observe that Armenians form a distinctive cluster bounded by Europeans, Near Easterners, and the Caucasus populations. More specifically, Armenians are close to (1) Spaniards, Italians, and Romanians from Europe; (2) Lebanese, Jews, Druze, and Cypriots from the Near East; and (3) Georgians and Abkhazians from the Caucasus (Figure 2b). The position of the Armenians within the global genetic diversity appears to mirror the geographical location of Turkey. Previous genetic studies have generally used Turks as representatives of ancient populations from Turkey. Our results show that Turks are genetically shifted towards Central Asians, a pattern consistent with a history of mixture with populations from this region.

Figure 2 Principal component analysis of >240 000 SNPs showing the top two components. (a) The position of Armenians in a global genetic diversity sample based on 78 populations from 11 geographical regions. Armenians (173 individuals) were projected to the plot and therefore did not contribute to the observed global structure. (b) A magnification shows that the Armenians (red) demonstrate genetic continuity with the Near East, Europe, and the Caucasus. Full size image

These diversity patterns observed in the PCA motivated formal testing of admixture in Armenians and other regional populations.

Admixture in the Near East

To formally test for population mixture in Armenians, we performed a 3-population test25 in the form of f3(Armenian; A, B), where a significantly negative value of the f3 statistic implies that Armenians descend from a mixture of the populations represented by A and B, chosen from the 78 global populations. We found signals of mixture from several African and Eurasian populations (Table 1, Figure 3). The most significantly negative f3 statistics are from a mixture of populations related to Sardinians and Central Asians, followed by several mixtures of populations from the Caucasus, Arabian Peninsula, the Levant, Europe, and Africa. We sought to date these mixture of events using exponential decay of admixture-induced LD. The oldest mixture events appear to be between populations related to sub-Saharan Africans and West Europeans occurring ~3800 bce, followed closely by a mixture of Sardinian and Caucasus-related populations. Later, several mixture events occurred from 3000 to 1200 bce involving diverse Eurasian populations (Table 1, Figure 3).

Figure 3 Genetically inferred source populations for Armenians, admixture times and genetic structure. Admixture events were estimated using decay of linkage disequilibrium with regional populations as sources for Armenians. Each horizontal coloured line indicates an admixture event and its width reflects the estimated date of admixture and SE. The plot also shows the estimated date of establishment of genetic structure within Armenians (1494–1545 CE). Major historical events and cultural developments in the Near East are shown at the bottom. Full size image

We compared the patterns of admixture in Armenians with those of other regional populations and detected signals of recent admixture in most other populations. For example, we find 7.9% (±0.4) East Asian ancestry in Turks from admixture occurring 800 (±170) years ago. We also detect sub-Saharan African gene flow 850 (±85) years ago in Syrians, Palestinians and Jordanians.

Structure of the Armenian population

To investigate the presence of genetic structure within the Armenian population, we performed model-based clustering on the values of the Armenian samples from the global PCA. The BIC computed by MCLUST suggests the best model to classify the Armenians is λ k A (diagonal distribution, variable volume, and equal shape) with three components (clusters). We observe the following: (1) Armenians in the diaspora that trace their origin to historical Western Armenia (modern-day East Turkey) form one group (Supplementary Figure S1, Cluster 1). (2) Armenians in modern-day Armenia (historical Eastern Armenia) are split into two major groups: 33% form Cluster 1 and 57% form Cluster 2 (Supplementary Figure S1). This structure could be the result of the Western Armenians’ migration to the East after the events of 1915 CE that displaced the entire Western Armenian population. (3) A few Armenians recruited from Chambarak and Maykop (Republic of Adygea, Russia) form an outlier to the two major Armenian clusters (Supplementary Figure S1, Cluster 3).

We investigated Armenian structure further using a procedure called ‘chromosome painting',15 which reconstructs the haplotype of every individual (receiver) in a data set using the haplotypes of other individuals (donors) in the data set. We then constructed a tree that infers population relationships and similarities (Supplementary Figure S2). We found, similarly to our previous clustering results, a fine genetic structure that splits Armenians into two major groups that are more similar to each other than to any other global population. The node containing most Armenians is deep compared with many other nodes containing several diverse regional populations. This probably reflects a prolonged isolation of the Armenians from their surrounding populations as suggested by the LD-based admixture tests.

We estimate from the LD patterns that divergence between the two major Armenian groups started 450–575 years ago (Figure 3).

Relationship to ancient Europeans

We merged our data set with the genome of the Tyrolean Iceman, a 5300-year-old individual discovered on the Italian part of the Ötztal Alps. We used TreeMix19 to construct a tree of genetic relationships using representative regional populations plus Armenians and Turks from the Near East. TreeMix uses a model that allows for both population splits and gene flow to better capture historical relationships between populations. We obtained a tree that recapitulates the known relationships among population groups. Furthermore, the tree shows that the Iceman shared drift with Sardinians, as previously reported.21 We then ran TreeMix allowing it to infer only one migration event, and revealed gene flow from the Iceman to Armenians, accounting for about 29% of their ancestry. The graph structure appeared robust in 100 bootstrap replicates with the first migration (highest weight and lowest P-value), always leading from the Iceman to Armenians (Figure 4).

Figure 4 Inferred population tree with one mixture event. The graph was inferred by TreeMix allowing one migration event. The migration arrow is coloured according to its weight; the weight is correlated with the ancestry fraction and shows that 29% of Armenian ancestry is derived from a population related to ancient Europeans. The graph is stable in 100 bootstrap replicates. Full size image

This structure was further investigated using outgroup f3 statistics.3, 18 The expected value of f3(Yoruba; Iceman, X) in the absence of admixture with Yoruba will be a function of the shared genetic history of the Iceman and X (non-African populations). Most shared ancestry of the Iceman is with Sardinians and other Europeans (Supplementary Figure S3). This is followed by shared ancestry with some Near Eastern populations: Cypriots, Sephardic Jews, Armenians, and Lebanese Christians. Other Near Easterners such as Turks, Syrians, and Palestinians show less shared ancestry with the Iceman.

To investigate if the affinity of the Near East genetic isolates to Europeans preceded the arrival of the early farmers to Europe (represented by the Iceman), we repeated the outgroup f3 statistics and replaced the Iceman with a 7000-year-old European hunter-gatherer from Spain (La Braña).24 West European hunter-gatherers have previously been shown to have contributed ancestry to all Europeans but not to Near Easterners.6 Consistent with this, we found reduced affinity and no noticeable structure in the Near Easterners in their relation to La Braña (Supplementary Figure S4; compared with the Iceman).