Origins of Greek Civilization: Minoans and Mycenaeans

Genetic affinity with Neolithic and modern European populations
The Minoan mtDNA haplotypes resembled those of the European populations (Figs 2b, 3a and 4; Supplementary Figs S1–S3). The majority of Minoans were classified in haplogroups H (43.2%), T (18.9%), K (16.2%) and I (8.1%). Haplogroups U5A, W, J2, U, X and J were each identified in a single individual. The greatest percentage of shared Minoan haplotypes was observed with European populations, particularly with individuals from Northern and Western Europe (26.98% and 29.28%, respectively) (Figs 2, 3, 4; Supplementary Table S7). Notably, in Fig. 4, a gradient can be observed, with the lowest affinity for Minoans found with Northern African populations and the percentage of haplotype sharing increasing as we move through the Middle East, Caucasus and the Mediterranean islands, southern Europe and mainland Europe (Fig. 4a). Of notice also is the high percentage of haplotype sharing with Bronze Age (Fig. 4c) and Neolithic (Fig. 4d) European populations.


Figure 4: Sharing of Minoan haplotypes with modern and ancient populations.

To apply PCA, each population was summarized by a frequency vector, depicting the frequency of each allele at each of the studied loci of the HVS-1 sequence. Pairwise distances between studied populations were computed based on the frequency vectors (using the standard L1 metric to measure distances between distributions), and the singular value decomposition of the resulting distance matrix was computed. The first two principal components capture >98% of the variation in the data and were deemed significant. Figure 5 illustrates the close relationship between the Minoans and the modern European populations. Importantly, three of the top ten nearest neighbours to the Minoans are ancient (two Neolithic and one Bronze Age) populations (Figs 5 and 6a, Table 1 and Supplementary Table S6). In fact, the highest percentage of Minoan haplotype sharing (33.33%) is observed with Neolithic populations from Southern Europe (including samples from Neolithic sites of Treilles and Iberia) (Fig. 4d).


Figure 5: Principal component analysis.

Our results strongly suggest that the principal matrilineal genetic relationships of the Minoans are with Neolithic, ancient and modern European populations. Such findings are in support of the hypothesis of an autochthonous origin of the Minoan civilization by the descendants of the Neolithic settlers of the island4,13. As it has been proposed for the other Neolithic European populations21,22,23, the most likely origin of the Cretan Neolithic settlers was Anatolia and the Middle East4,7,9,10,11. Given that the timing of the first Neolithic inhabitants to reach Crete 9,000 YBP coincides with the migration of Neolithic farmers out of Anatolia3, it is highly probable that the same ancestral population that spread to Europe, also spread to Crete and contributed to the founding of the early Minoan civilization. It has been suggested24 that in addition to agricultural methods, the Anatolian farmers also brought with them the Indo-European language25,26. The current prevailing hypothesis is that the Minoan language was unrelated to the Indo-European family. Alternatively, as suggested by Renfrew5, Proto-Minoan was one of the branches derived from the Proto-Indo-European language about 9,000 YBP.


Figure 6: Relationships between the Minoans and other European populations.

The PCA analysis also highlights the high affinity of the Minoans to the current inhabitants of the Lassithi plateau as well as Greece. Among the top 10 nearest neighbours to our Minoan population sample, four are Greek populations and two of these from Lassithi prefecture (Fig. 5). The close relationship of the Minoans to modern Cretans is also apparent, when analysis is restricted to populations originating from Greece (Fig. 6b). Particularly in respect to the first PCA (capturing 92% of the variance of this particular subset of the data), the Minoans are extremely close to the modern Lassithi population, the populations from the islands of Chios and Euboea, as well as the populations of Argolis and Lakonia (Southern Greece ) (Fig. 6b). Thus, the modern inhabitants of the Lassithi plateau still carry the maternal genetic signatures of their ancient predecessors of the Minoan population.

Nature Communications volume 4, Article number: 1861 (2013)

Beyond the visual impressions of PCA and ADMIXTURE, we formally tested the relationships between populations from our study and the literature, using f4-statistics of the form f4(X, Y; Test, Chimp) that evaluate whether Test shares more alleles with X or Y. We find that Test populations from Iran, the Caucasus, and eastern Europe share more alleles with Minoans and Mycenaeans than with the Neolithic population of Greece (Extended Data Fig. 2a,b). The Minoans from the Lasithi plateau in the highlands of eastern Crete and from the coast of southern Crete (Extended Data Fig. 2c) are consistent with being a homogeneous population. Mycenaeans differ from these Minoans in sharing significantly fewer alleles with Neolithic people from the Levant, Anatolia, Greece, and mainland Europe (Extended Data Fig. 2d). In comparison, the Bronze Age Anatolians share fewer alleles with ancient Europeans and more with ancient populations of Iran and the Levant (Extended Data Fig. 3). We used f3-statistics of the form f3(Ref1, Ref2; Test) which, if negative, show that Test is admixed from sources related to the Ref1, Ref2 source populations. We do not find significantly negative (Ref1, Ref2) pairs for Minoans or Bronze Age Anatolians (Z>−2.5), but do for Mycenaeans (−4.9<Z<−3.0; Extended Data Fig. 4), involving early farmers from the Levant, Anatolia, Greece, and the rest of Europe as one source, and Iran or the Eurasian steppe or steppe-influenced Europeans as the other.


Figure 2: Genetic differentiation of Bronze Age populations to present-day populations.

We modelled Bronze Age populations using qpAdm/qpWave6 framework (Methods; Supplementary Information, section 2) which relates a set of ‘left’ populations (admixed population and ancestral source populations) with a set of ‘right’ populations (diverse outgroups) and allows one to test for the number of streams of ancestry from ‘right’ to ‘left’ and to estimate admixture proportions. This analysis shows that all Bronze Age populations from the Aegean and Anatolia derived most (~62–86%) of their ancestry from an Anatolian Neolithic-related population (Table 1). However, they also had a component (~9–32%) of ‘eastern’ (Caucasus/Iran-related) ancestry. It was previously shown that this type of ancestry was introduced into mainland Europe via Bronze Age pastoralists from the Eurasian steppe who were a mix of both eastern European hunter-gathers and populations from the Caucasus and Iran4,6; our results show that it also arrived on its own, at least in the Minoans, without eastern European hunter-gatherer ancestry. This ancestry need not have arrived from regions east of Anatolia, as it was already present during the Neolithic in central Anatolia at Tepecik-Çiftlik17 (Supplementary Information, section 2). The eastern influence in the Bronze Age populations from Greece and southwestern Anatolia is also supported by an analysis of their Y-chromosomes. Four out of five males belonging to Minoans, Mycenaeans, and southwestern Anatolians (Supplementary Information, section 3) belonged to haplogroup J which was rare or non-existent in earlier populations from Greece and western Anatolia which were dominated by Y-chromosome haplogroup G21,2,17. Haplogroup J was present in Caucasus hunter-gatherers3 and a Mesolithic individual from Iran4 and its spread westward may have accompanied the ‘eastern’ genome-wide influence.

The Minoans could be modelled as a mixture of the Anatolia Neolithic-related substratum with additional ‘eastern’ ancestry, but the other two groups had additional ancestry: the Mycenaeans had ~4–16% ancestry from a ‘northern’ ultimate source related to the hunter-gatherers of eastern Europe and Siberia (Table 1), while the Bronze Age southwestern Anatolians may have had ~6% ancestry related to Neolithic Levantine populations. The elite Mycenaean individual from the ‘royal’ tomb at Peristeria in the western Peloponnese did not differ genetically from the other three Mycenaean individuals buried in common graves. To identify more proximate sources of the distinctive eastern European/north Eurasian-related ancestry in Mycenaeans, we included later populations as candidate sources (Supplementary Information, section 2), and could model Mycenaeans as a mixture of the Anatolian Neolithic and Chalcolithic-to-Bronze Age populations from Armenia (Table 1). Populations from Armenia possessed some ancestry related to eastern European hunter-gatherers4, so they, or similar unsampled populations of western Asia, could have contributed it to populations of the Aegean. This model makes geographical sense, since a population movement from the vicinity of Armenia could have admixed with Anatolian Neolithic-related farmers on either side of the Aegean. However, Mycenaeans can also be modelled as a mixture of Minoans and Bronze Age steppe populations (Table 1; Supplementary Information, section 2), suggesting that, alternatively, ‘eastern’ ancestry arrived in both Crete and mainland Greece, followed by ~13–18% admixture with a ‘northern’ steppe population in mainland Greece only. Such a scenario is also plausible: first, it provides a genetic correlate for the distribution of shared toponyms in Crete, mainland Greece, and Anatolia discovered by Kretschmer21; second, it postulates a single migration from the east; third, it proposes some gene flow from geographically contiguous areas to the north where steppe ancestry was present since at least the mid-3rd millennium BCE6,9. We validated inferences from qpAdm by treating source populations as ‘ghosts’ and re-estimating mixture proportions4, by examining the correspondence between qpAdm estimates and PCA4 (Extended Data Fig. 5), and by comparing simulated individuals of known ancestry against the Mycenaeans (Extended Data Fig. 6).


Extended Data Figure 1: ADMIXTURE analysis.

Geographical structure may have prevented the spread of the ‘northern’ ancestry from the mainland to Crete, contributing to genetic differentiation. Such structure may, in principle, be long-standing, even prior to the advent of the Neolithic in the 7th millennium BCE. Alternatively, both ‘northern’ and ‘eastern’ ancestry may have arrived in the Aegean at any time between the Early Neolithic and the Late Bronze Age. Wider geographical and temporal sampling of pre-Bronze Age populations of the Aegean may better trace the advent of ‘northern’ and ‘eastern’ ancestry in the region. However, sampled Neolithic samples from Greece, down to the Final Neolithic ~4,100 BCE2, do not possess either type of ancestry, suggesting that the admixture we detect probably occurred during the 4th–2nd millennium BCE time window.

Other proposed migrations, such as settlement by Egyptian or Phoenician colonists22 are not discernible in our data, as there is no measurable Levantine or African influence in the Minoans and Myceneans, thus rejecting the hypothesis that the cultures of the Aegean were seeded by migrants from the old civilizations of these regions. On the other hand, migrants from areas east or north of the Aegean, while numerically less influential than the locals, may have contributed to the emergence of the 3rd–2nd millennium BCE Bronze Age cultures as ‘creative disruptors’ of local traditions, bearers of innovations, or through cultural interaction with the locals, coinciding with the genetic process of admixture.23 Relative ancestral contributions do not determine the relative roles in the rise of civilization of the different ancestral populations, but, nonetheless, the strong persistence of the Neolithic substratum does suggest a key role for the locals in this process.


Extended Data Figure 7: FST between Bronze Age and present-day West Eurasian populations.

Phenotype prediction from genetic data has enabled the reconstruction of the appearance of ancient Europeans1,24 who left no visual record of their pigmentation. By contrast, the appearance of the Bronze Age people of the Aegean has been preserved in colourful frescos and pottery, depicting people with mostly dark hair and eyes25. We used the HIrisPlex26 tool (Supplementary Information, section 4) to infer that the appearance of our ancient samples matched the visual representations (Extended Data Table 2), suggesting that art of this period reproduced phenotypes naturalistically.

We estimated FST of Bronze Age populations with present-day West Eurasians, finding that Mycenaeans are least differentiated from populations from Greece, Cyprus, Albania, and Italy (Fig. 2), part of a general pattern in which Bronze Age populations broadly resemble present-day inhabitants from the same region (Extended Data Fig. 7). Modern Greeks occupy the intermediate space of the PCA along PC1 (Fig. 1b) between ancient European and Near Eastern populations, like the ones of the Bronze Age. They are not, however, identical to Bronze Age populations, as they are above them along PC2 (Fig. 1b). This is due to the fact that Neolithic farmers share fewer alleles with Modern Greeks than with Mycenaeans (Extended Data Fig. 8), consistent with additional later admixture27,28.

Nature. 2017 Aug 10; 548(7666): 214–218.