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Post by Admin on Aug 17, 2017 19:03:03 GMT
 The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean1, 2, and most of the remainder from ancient populations related to those of the Caucasus3 and Iran4, 5. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter–gatherers of eastern Europe and Siberia6, 7, 8, introduced via a proximal source related to the inhabitants of either the Eurasian steppe1, 6, 9 or Armenia4, 9. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations. We performed principal component analysis (PCA)20 (Methods), projecting ancient samples onto the first two principal components inferred from present-day West Eurasian populations10 that form two south–north parallel clines in Europe and the Near East along principal component 2. Minoans and Mycenaeans were centrally positioned in the PCA (Fig. 1b), framed to the left by ancient populations from mainland Europe and the Eurasian steppe, to the right by ancient populations from the Caucasus and Western Asia, and to the bottom by Early/Middle Neolithic farmers from Europe and Anatolia. The Neolithic samples from Greece clustered with these farmers and were distinct from the Minoans and Mycenaeans. The Bronze Age individuals from southwestern Anatolia were also distinct, intermediate between Anatolian and Levantine populations towards the bottom, and populations from Armenia, Iran, and the Caucasus towards the top.  We modelled Bronze Age populations using the qpAdm/qpWave6 framework (Methods and 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 testing for the number of streams of ancestry from ‘right’ to ‘left’ and estimation of admixture proportions. This analysis showed that all Bronze Age populations from the Aegean and Anatolia are consistent with deriving most (approximately 62–86%) of their ancestry from an Anatolian Neolithic-related population (Table 1). However, they also had a component (approximately 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–gatherers 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 who were dominated by Y-chromosome haplogroup G2 (refs 1, 2, 17). Haplogroup J was present in Caucasus hunter–gatherers3 and a Mesolithic individual from Iran4, and its spread westwards may have accompanied the ‘eastern’ genomewide 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 approximately 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 and Supplementary Information section 2), suggesting that, alternatively, ‘eastern’ ancestry arrived in both Crete and mainland Greece, followed by about 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 in ref. 21; 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-third millennium bc (refs 6, 9). |
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Post by Admin on Aug 19, 2017 19:55:35 GMT
 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 Mycenaeans, 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 third to second millennium bc 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 admixture23. Relative ancestral contributions do not determine the relative roles in the rise of civilization of the different ancestral populations; nonetheless, the strong persistence of the Neolithic substratum does suggest a key role for the locals in this process. 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 the fixation index, FST, of Bronze Age populations with present-day West Eurasians, finding that Mycenaeans were least differentiated from populations from Greece, Cyprus, Albania, and Italy (Fig. 2), part of a general pattern in which Bronze Age populations broadly resembled present-day inhabitants from the same region (Extended Data Fig. 7). Modern Greeks occupy the intermediate space of the PCA along principal component 1 (Fig. 1b) between ancient European and Near Eastern populations, such as those of the Bronze Age. They are not, however, identical to Bronze Age populations, as they are above them along principal component 2 (Fig. 1b). This is because Neolithic farmers shared fewer alleles with Modern Greeks than with Mycenaeans (Extended Data Fig. 8), consistent with additional later admixture27,28. The Minoans and Mycenaeans, sampled from different sites in Crete and mainland Greece, were homogeneous, supporting the genetic coherency of these two groups. Differences between them were modest, viewed against their broad overall similarity to each other and to the southwestern Anatolians, sharing in both the ‘local’ Anatolian Neolithic-like farmer ancestry and the ‘eastern’ Caucasus-related admixture. Two key questions remain to be addressed by future studies. First, when did the common ‘eastern’ ancestry of both Minoans and Mycenaeans arrive in the Aegean? Second, is the ‘northern’ ancestry in Mycenaeans due to sporadic infiltration of Greece, or to a rapid migration as in Central Europe6 ? Such a migration would support the idea that proto-Greek speakers29 formed the southern wing of a steppe intrusion of Indo-European speakers. Yet, the absence of ‘northern’ ancestry in the Bronze Age samples from Pisidia, where Indo-European languages were attested in antiquity, casts doubt on this genetic– linguistic association, with further sampling of ancient Anatolian speakers needed. Whatever the answer to these questions, the discovery of at least two migration events into the Aegean in addition to the first farming dispersal before the Bronze Age, and of additional population change since that time, supports the view that the Greeks did not emerge fully formed from the depths of prehistory, but were, indeed, a people ‘ever in the process of becoming’30."  Nature (2017) doi:10.1038/nature23310 |
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Post by Admin on Oct 20, 2017 19:14:39 GMT
 The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence. The petrous bone and differential DNA yields Although the advantages of genome-wide analysis are numerous, such data have not been routinely accessible due to the typically low endogenous DNA content in human bones in most archaeological contexts1,2,3. We compared endogenous DNA content from the petrous portion of the temporal bone, the densest bone in the mammalian body17, and paired alternate skeletal elements from six Hungarian skeletons sampled across diverse time depths (Fig. 1 and Supplementary Table 2). The endogenous DNA yields from the petrous samples exceeded those from the teeth by 4- to 16-fold and those from other bones up to 183-fold. Thus, while other skeletal elements yielded human, non-clonal DNA contents ranging from 0.3 to 20.7%, the levels for petrous bones ranged from 37.4 to 85.4% (Fig. 1). We extended this sampling to a further seven petrous bones from Hungary and yields of endogenous DNA remained exceptionally and consistently high (Supplementary Table 3).  Figure 1: Petrous bones versus non-petrous bones. Temporal dynamics of genomic affinity All analyzed individuals are from defined archaeological contexts from the onset of agriculture in this region during the Early Neolithic Körös period through to the pre-Scythian Iron Age and were directly radiocarbon dated (Table 1). To assess genomic continuity versus change in this time series and to determine how these ancient genomes relate to each other, to other ancient European genomes and to modern-day human populations, we generated a two-dimensional summary of autosomal genomic variation using principal components analysis (PCA) and combined our observed genotype data with published ancient sequences and genotypes of 552 modern individuals from Europe, Caucasus and the Near East1,2,6,18,19,20. Individual plots, similar in resolution to those observed in analyses of full modern single nucleotide polymorphism (SNP) data sets, were subsequently combined into a single plot using Procrustes transformation, following the study by Skoglund et al.2 This analysis shows clear shifts (including two within multi-phased archaeological sites) in the genomic affinities of the ancient genotypes coinciding with cultural shifts and bracketing a 2,800 year period of Neolithic stasis. Although our sampling is concentrated in the first millennium of this interval, to place a particular emphasis on the Neolithisation process in Southeast/Central Europe, it was constructed to include material from the diverse archaeological phases within the Hungarian Neolithic. Based on these analyses, our samples can be divided into four sets that are located in different regions of the PCA. Our oldest sample, Körös Neolithic (KO1) (5,650–5,780 cal BC) was excavated from a short-lived agricultural settlement, perhaps spanning only two generations, at the northern range limit of the first Neolithic (Körös) cultural complex in Southeast Europe21. Despite its early Neolithic farming context, this genome falls towards the hunter-gatherer vicinity of the PCA plot (Fig. 2). In contrast, sample KO2, which is contemporaneous to KO1 (5,570–5,710 cal BC) and also from a Neolithic Körös Culture site only ~70 km distant, clusters with later Neolithic individuals (Fig. 2 and Supplementary Fig. 1).This marked genomic dichotomy between KO1 and KO2 suggests direct contact between indigenous hunter-gatherers and Neolithic communities as suggested previously2,8,22. The outlying Neolithic individual, KO1, was a blue-eyed male (Fig. 3) and his Y-chromosome lineage, I2a, matches the only haplogroup reported to date in Mesolithic Central and Northern Europeans5,8 (n=6). |
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Post by Admin on Oct 21, 2017 20:07:32 GMT
 Figure 2: PCA of the ancient Hungarian time series. Our Neolithic genomes all cluster with affinity to Southern Mediterranean individuals, particularly Sardinians, echoing the results of previous direct analyses of European Neolithic and post-Neolithic genomes2,6,8. This affinity persists through nine successive time points in our data, including a diversity of Neolithic cultures. In contrast, we observe high mtDNA diversity during this period, as previously observed in Central Europe23. Affinities of our observed Y-chromosome lineages (I2 and C6 haplogroups, Table 1) with a Mesolithic background5,7 and our mtDNA haplogroups with farming communities (especially the N1a haplogroup, Table 1)24 tentatively support the incorporation of local male hunter-gatherers into farming communities during the Central European Neolithic (Table 1), in contrast to the male-dominated diffusion of farmers suggested for the Mediterranean route. The genomic stasis of the Neolithic is subsequently interrupted during the third millennium BC coinciding with the onset of the Bronze Age. Our two Bronze Age samples, BR1 (1,980–2,190 cal BC) and BR2 (1,110–1,270 cal BC) fall among modern Central European genotypes. Within this period the trade in commodities across Europe increased and the importance of the investigated region as a node is indicated by the growth of heavily fortified settlements in the vicinities of the Carpathian valleys and passes linking North and South26. These two Bronze Age genomes represent the oldest genomic data sampled to date with clear Central European affinities. A third genomic shift occurs around the turn of the first millennium BC. The single Iron Age genome, sampled from the pre-Scythian Mezőcsát Culture (Iron Age (IR1), 830–980 cal BC), shows a distinct shift towards Eastern Eurasian genotypes, specifically in the direction of several Caucasus population samples within the reference data set. This result, supported by mtDNA and Y-chromosome haplogroups (N and G2a1, respectively, both with Asian affinities) suggests genomic influences from the East. This is supported by the archaeological record which indicates increased technological and typological affinities with Steppe cultures at this time, including the importation of horse riding, carts, chariots and metallurgical techniques26. Modern Hungarians occupy an intermediate position between the IR1 and more Western Bronze Age genomes, most likely reflecting the continuation of admixture in the Central European gene pool since this time.  Figure 3: Selective sweeps. Our Neolithic genomes all cluster with affinity to Southern Mediterranean individuals, particularly Sardinians, echoing the results of previous direct analyses of European Neolithic and post-Neolithic genomes2,6,8. This affinity persists through nine successive time points in our data, including a diversity of Neolithic cultures. In contrast, we observe high mtDNA diversity during this period, as previously observed in Central Europe23. Affinities of our observed Y-chromosome lineages (I2 and C6 haplogroups, Table 1) with a Mesolithic background5,7 and our mtDNA haplogroups with farming communities (especially the N1a haplogroup, Table 1)24 tentatively support the incorporation of local male hunter-gatherers into farming communities during the Central European Neolithic (Table 1), in contrast to the male-dominated diffusion of farmers suggested for the Mediterranean route25. The genomic stasis of the Neolithic is subsequently interrupted during the third millennium BC coinciding with the onset of the Bronze Age. Our two Bronze Age samples, BR1 (1,980–2,190 cal BC) and BR2 (1,110–1,270 cal BC) fall among modern Central European genotypes. Within this period the trade in commodities across Europe increased and the importance of the investigated region as a node is indicated by the growth of heavily fortified settlements in the vicinities of the Carpathian valleys and passes linking North and South26. These two Bronze Age genomes represent the oldest genomic data sampled to date with clear Central European affinities. A third genomic shift occurs around the turn of the first millennium BC. The single Iron Age genome, sampled from the pre-Scythian Mezőcsát Culture (Iron Age (IR1), 830–980 cal BC), shows a distinct shift towards Eastern Eurasian genotypes, specifically in the direction of several Caucasus population samples within the reference data set. This result, supported by mtDNA and Y-chromosome haplogroups (N and G2a1, respectively, both with Asian affinities) suggests genomic influences from the East. This is supported by the archaeological record which indicates increased technological and typological affinities with Steppe cultures at this time, including the importation of horse riding, carts, chariots and metallurgical techniques26. Modern Hungarians occupy an intermediate position between the IR1 and more Western Bronze Age genomes, most likely reflecting the continuation of admixture in the Central European gene pool since this time. |
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Post by Admin on Oct 23, 2017 19:18:01 GMT
 Figure 4: Ancient Hungarians ADMIXTURE plot. Imputation of ancient genomes The information content of low-coverage genome sequences may be leveraged using imputation with a phased reference panel to achieve genome-wide diploid genotypes and enable richer data analyses27. To test this approach in the context of palaeogenomic data we used the 1,000 Genomes Project phased reference data to impute 5,309 and 6,159 well-characterized SNP genotypes on chromosome 22 from a range of downsampled coverage levels of NE1 and BR2, respectively, and compared calls with those made directly from their full genome data (Supplementary Methods)27,28. Considering an imputed 1 × sample of NE1 and imposing a genotype probability threshold of 0.99, 78% of these loci remained, with diminishing return from increasing coverage in the subsample (Supplementary Fig. 5). Of the imputed genotypes, 99.20% (99.18% of heterozygotes) matched the observed high-coverage calls, validating this approach for expanding our data (Supplementary Figs 5–9). With the more recent BR2 genome, imputation from 1 × coverage allowed 80.0% of loci to be called at a 0.99 thereshold with 99.33% (99.05% of heterozygotes) match to high-coverage calls. Therefore, we imputed genome-wide genotypes for each of the low-coverage genomes and, after intersection with modern SNP data, called a total of 151,407 high-quality diploid loci across all samples. These data were used in an ADMIXTURE analysis29, which reaffirmed the clustering and temporal shifts in affinity observed in the PCA visualization (Fig. 4).  Figure 5: Short versus long ROH. These data also allowed us to estimate the fraction of each genome under runs of homozygosity30 (Fig. 5), which gives information about past demography. Long contiguous homozygous segments within a genome are indicative of recent endogamy while shorter runs result from older manifestations of small ancestral population size31. Unlike a small subset of modern genomes, no ancient genome in our analysis showed a clear excess of long runs of homozygosity (ROH) (>1.6 Mb), suggesting each to have been outbred. However, a clear temporal trend was evident in the extent of ROH, especially shorter ROH, with the Bronze Age and IR1 individuals falling within the bulk of modern values, Neolithic specimens tending towards the upper end of this range and the Early Neolithic Körös specimen, KO1 forming a clear outlier. This suggests an unusually restricted ancestral population size for KO1 (we note that low heterozygosity was also found within a 8,000 year old hunter-gatherer from Luxembourg5), supporting the inference that he represents an exogenous individual in a farming settlement. A possible criticism of this approach is that bias against heterozygous calls and the existence of ancient haplotypes that are absent from the reference genomes may impede analyses built on imputed data; our high-coverage ancient Neolithic genome, NE1, falls outside PCA clusters of the 1,000 Genomes reference individuals, along with our KO1 and IR1 samples (Supplementary Fig. 8). Therefore, we further analyzed genome-wide imputations of 0.5 × , 1 × and 2.5 × coverage samples of the NE1 and BR2 genomes. In both PCA and ROH plots of genotypes from these, the positions from each replicate were highly similar to those generated from high-coverage SNP calls (Supplementary Figs 6 and 7). |
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