A story of 69 ancient Europeans

A new study on the bioRxiv includes data on 69 ancient Europeans (remember when we got excited in anticipation for the single genome of the Iceman? that was only three years ago) and adds plenty of new info to chew on for those of us interested in prehistory. 

Two Near Eastern migrations into Europe

In 2011, I observed that West Eurasian populations were too close (measured by Fst) to allow for long periods of differentiation between them. By implication, there must have been a "common source" of ancestry uniting them, which I placed in a "womb of nations" of the Neolithic Near East. I proposed that migrations out of this core area homogenized West Eurasians, writing:

In Arabia, the migrants would have met aboriginal Arabians, similar to their next door-neighbors in East Africa, undergoing a subtle African shift (Southwest_Asians). In North Africa, they would have encountered denser populations during the favorable conditions of MIS 1, and by absorbing them they would became the Berbers (Northwest_Africans). Their migrations to the southeast brought them into the realm of Indian-leaning people, in the rich agricultural fields of the Mehrgarh and the now deserted oases of Bactria and Margiana. Across the Mediterranean and along the Atlantic facade of Europe, they would have encountered the Mesolithic populations of Europe, and through their blending became the early Neolithic inhabitants of the Mediterranean and Atlantic coasts of Europe (Mediterraneans). And, to the north, from either the Balkans, the Caucasus, or the trans-Caspian region, they would have met the last remaining Proto-Europeoid hunters of the continental zone, becoming the Northern Europeoids who once stretched all the way to the interior of Asia.

The new paper confirms the last two of these migrations. The remainder involve parts of the world from which no ancient DNA has been studied.

The first migration (early Neolithic) is already uncontroversial, but the paper includes data from Spanish early farmers that are also Sardinian- and LBK-like. The "Sardinian" Iceman was no fluke. It is now proven that not only the LBK but also the Spanish Neolithic came from the same expansion of Mediterranean populations which survives in Sardinia. The authors write:

Principal components analysis (PCA) of all ancient individuals along with 777 present-day West Eurasians4 (Fig. 2a, SI5) replicates the positioning of present-day Europeans between the Near East and European hunter-gatherers4,20, and the clustering of early farmers from across Europe with present day Sardinians3,4,27, suggesting that farming expansions across the Mediterranean to Spain and via the Danubian route to Hungary and Germany descended from a common stock.

The second migration went into eastern Europe:

The Yamnaya differ from the EHG by sharing fewer alleles with MA1 (|Z|=6.7) suggesting a dilution of ANE ancestry between 5,000-3,000 BCE on the European steppe. This was likely due to admixture of EHG with a population related to present-day Near Easterners, as the most negative f3-statistic in the Yamnaya (giving unambiguous evidence of admixture) is observed when we model them as a mixture of EHG and present-day Near Eastern populations like Armenians (Z = -6.3; SI7).

The EHG (Eastern European Hunter-Gatherers) are likely Proto-Europeoid foragers and the Yamnaya (a Bronze Age Kurgan culture) were a mixture of the EHG and something akin to Armenians.The "attraction" of later groups to the Near East is clear in the PCA: hunter-gatherers on the left side, the Near East (as grey dots) on the right side, and Neolithic/Bronze Age/modern Europeans in the middle. The second migration may very well be related to the Uruk expansion and the presence of gracile Mediterranoids and robust Proto-Europeoids in the Yamna:

The Yamna population generally belongs to the European race. It was tall (175.5cm), dolichocephalic, with broad faces of medium height. Among them there were, however, more robust elements with high and wide faces of the proto-Europoid type, and also more gracile individuals with narrow and high faces, probably reflecting contacts with the East Mediterranean type (Kurts 1984: 90).

The authors present a table of Fst values which confirms the homogenizing influence of migrations from the Near East. The WHG group has an Fst=0.086 with Armenians, but the LBK farmers have only 0.023. The EHG group has an Fst=0.067 with Armenians, but the Yamnaya steppe people have only 0.030. Someone might argue that it is the Armenians that are receiving genes from Europe, but the same pattern holds even for the Bedouins, for which admixture with Europeans seems far-fetched: 0.106 to 0.043 and 0.093 to 0.060. It is now clear that the "glue" that did not allow West Eurasian populations to drift very far apart were migrations from the Near East.

The (partial) demise of the farmers

It seems that the legacy of the early farmers suffered two hits, which is why only in Sardinia and (to a lesser degree) in southern Europe that they have persisted as the major component of ancestry. The first blow came during the Neolithic:

Middle Neolithic Europeans from Germany, Spain, Hungary, and Sweden from the period ~4,000-3,000 BCE are intermediate between the earlier farmers and the WHG, suggesting an increase of WHG ancestry throughout much of Europe.

And the coup de grâce after the 5kya mark:

We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG. The estimate of Yamnaya related ancestry in the Corded Ware is consistent when using either present populations or ancient Europeans as outgroups (SI9, SI10), and is 73.1 ± 2.2% when both sets are combined (SI10). [...] The magnitude of the population turnover that occurred becomes even more evident if one considers the fact that the steppe migrants may well have mixed with eastern European agriculturalists on their way to central Europe. Thus, we cannot exclude a scenario in which the Corded Ware arriving in today’s Germany had no ancestry at all from local populations.

Confirmation of the Bronze Age Indo-European invasion of Europe

In 2012 I had used the paltry data on a handful ancient DNA samples to observe that in ADMIXTURE modern Europeans had a West Asian genetic component (peaking in "Caucasus" and "Gedrosia") that pre-5kya Europeans didn't. I proposed that the Bronze Age migration of the Indo-Europeans spread this component:

But there is another component present in modern Europe, the West_Asian which is conspicuous in its absence in all the ancient samples so far. This component reaches its highest occurrence in the highlands of West Asia, from Anatolia and the Caucasus all the way to the Indian subcontinent. [...] Nonetheless, some of the legacy of the earliest Indo-European speakers does appear to persist down to the present day in the genomes of their linguistic descendants, and I predict that when we sample later (post 5-4kya) individuals we will finally find the West_Asian piece that is missing from the European puzzle.

This prediction is now confirmed:

This pattern is also seen in ADMIXTURE analysis (Fig. 2b, SI6), which implies that the Yamnaya have ancestry from populations related to the Caucasus and South Asia that is largely absent in 38 Early or Middle Neolithic farmers but present in all 25 Late Neolithic or Bronze Age individuals. This ancestry appears in Central Europe for the first time in our series with the Corded Ware around 2,500 BCE (SI6, Fig. 2b, Extended Data Fig. 1).

I was a little puzzled with the "Ancient North Eurasians" recently proposed as a "third ancestral population" for Europeans: it seemed to be a tertium quid that spread after 5kya, but very different geographically than the "West Asian" component. But:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6).

So, it seems that there is no contradiction after all and both EHG (which is related to "Ancient North Eurasians") and another type of Near Eastern ancestry (=West_Asian) arrived after 5kya.

1939 strikes back

It is amazing how well this was anticipated by Carleton Coon in 1939. Back then much of West Eurasia was an archaeological/anthropological terra incognita, there was no radiocarbon dating, no DNA, no computers, not even serious multivariate statistics. And yet:

We shall see, in our survey of prehistoric European racial movements, 8 that the Danubian agriculturalists of the Early Neolithic brought a food-producing economy into central Europe from the East. They perpetuated in the new European setting a physical type which was later supplanted in their original home. Several centuries later the Corded people, in the same way, came from southern Russia but there we first find them intermingled with other peoples, and the cul-tural factors which we think of as distinctively Corded are included in a larger cultural equipment. [...] On the basis of the physical evidence as well, it is likely that the Corded people came from somewhere north or east of the Black Sea. The fully Neolithic crania from southern Russia which we have just studied include such a type, also seen in the midst of Sergi's Kurgan aggregation. Until better evidence is produced from elsewhere, we are entitled to consider southern Russia the most likely way station from which the Corded people moved westward.

And in 2015:

Our results support a view of European pre-history punctuated by two major migrations: first, the arrival of first farmers during the Early Neolithic from the Near East, and second of Yamnaya pastoralists during the Late Neolithic from the steppe (Extended Data Fig. 5).

In 1939:

Linguistically, Indo-European is probably a relatively recent phenomenon, which arose after animals had been tamed and plants cultivated. The latest researches find it to be a derivative of an initially mixed language, whose principal elements were Uralic, called element A, and some undesignated element B which was probably one of the eastern Mediterranean or Caucasic languages. 5 The plants and animals on which the Somewhere in the plains of southern Russia or central Asia, the blending of languages took place which resulted in Indo-European speech. This product in turn spread and split, and was further differentiated by mixture with the languages of peoples upon whom it, in one form or other, was imposed. Some of the present Indo-European languages, in addition to these later accretions from non-Indo-European tongues, contain more of the A element than others, which contain more of the B. The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete. 

In 2015:

These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6). We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG.

The EHG is still flimsy as it's only two individuals from Karelia and Samara who are very similar to each other. It's hard not to imagine that the hunter-gatherer from Russian Karelia (outside any proposed PIE homeland) would be speaking a similar language as his Samara counterpart. Did they both speak "element A" and was PIE formed when the "southern" steppe hunter-gatherers came into contact with "element B" people from the Caucasus? Short of a time machine, we can never say for sure. This might very well be an answer to the conundrum of Uralic/Proto-Kartvelian borrowings. There is simply no geographical locale in which these two language families neighbor each other: Northwest, Northeast Caucasian speakers and the pesky Greater Caucasus intervene. But, maybe there was no such locale, and these borrowings aren't due to some "PIE people" living adjacent to Uralic and Proto-Karvelian speakers but the "PIE people" being a mix of an element A (EHG) that was (or interacted with) Uralic and another element B (Armenian-like) that was (or interacted with) Proto-Kartvelian.

Urheimat (or not?)

The authors of the current paper are agnostic about the PIE homeland:

We caution that the location of the Proto-Indo-European9,27,29,30 homeland that also gave rise to the Indo-European languages of Asia, as well as the Indo-European languages of southeastern Europe, cannot be determined from the data reported here (SI11). Studying the mixture in the Yamnaya themselves, and understanding the genetic relationships among a broader set of ancient and present-day Indo-European speakers, may lead to new  insight about the shared homeland.

Whatever the ultimate answer will be, it seems that Coon was right that "The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete." If PIE=EHG (as Anthony and Ringe suggest), then "from the crib", PIE got half its ancestry from a non-IE, Near Eastern source. Conversely, if PIE=Near East (as I suggested) then "from the crib", PIE got half of its ancestry from a non-IE, Eastern European source. The "Yamnaya" seems to max out in Norwegians at around half, which means that they are about a quarter Proto-Indo-European genetically, regardless of which theory is right.

These two possibilities (as well as the third one of PIE being neither-nor, but rather a linguistic mixture of the languages of the EHG and Near East) are testable. The Anthony/Ringe version of the steppe hypothesis predicts pre-Yamnaya expansions from the steppe. Whether these happened and what was their makeup can be tested: if they did occur and they did lack "Near Eastern" ancestry, then the steppe hypothesis will be proven. PIE in the Near East, on the other hand, predicts that some PIE languages (certainly the Anatolian ones) will be a "within the Near East" expansion. If such migrations did occur and they lacked "EHG" ancestry, then some variant of the Gamkrelidze/Ivanov model will be proven. Or, the truth might be that everywhere where Indo-Europeans arrive they carry a blend of "West Asian" and "EHG", supporting the third possibility. Time will tell.

In the interim, I am curious about how much Yamnaya ancestry existed in different parts of Europe (all of the post-5kya samples in this study come from Germany, with a couple from Hungary). In northern Europe, all populations seem to have less Yamnaya ancestry than the Corded Ware: there it must have declined. But, modern Hungarians have more than Bronze Age Hungarians: there it must have increased.

Germany and a slice of Hungary is a very narrow window through which to see the whole of Europe and these results must be tested by looking at samples from beyond the "heartland". I do hope that some kind of Moore's law operates in the world of ancient DNA, and in three more years we'll be reading studies about thousands of ancient individuals.

bioRxiv doi: http://dx.doi.org/10.1101/013433
Massive migration from the steppe is a source for Indo-European languages in Europe

Wolfgang Haak , Iosif Lazaridis , Nick Patterson , Nadin Rohland , Swapan Mallick , Bastien Llamas , GuidoBrandt , Susanne Nordenfelt , Eadaoin Harney , Kristin Stewardson , Qiaomei Fu , Alissa Mittnik , Eszter Banffy ,Christos Economou , Michael Francken , Susanne Friederich , Rafael Garrido Pena , Fredrik Hallgren , ValeryKhartanovich , Aleksandr Khokhlov , Michael Kunst , Pavel Kuznetsov , Harald Meller , Oleg Mochalov ,Vayacheslav Moiseyev , Nicole Nicklisch , Sandra L. Pichler , Roberto Risch , Manuel A. Rojo Guerra , ChristinaRoth , Anna Szecsenyi-Nagy , Joachim Wahl , Matthias Meyer , Johannes Krause , Dorcas Brown , DavidAnthony , Alan Cooper , Kurt Werner Alt , David Reich

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Link

Ancient DNA from prehistoric inhabitants of Hungary

A very interesting new article on Europe describes new data from ancient Hungary from the Neolithic to the Iron Age. It is open access, so go ahead and read it. I will update this entry with some comments after I read the paper myself.

UPDATE I (The petrous bone):

The authors write:

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).

This seems like a very exciting technical breakthrough that will increase DNA yields in future studies.

UPDATE II (PCA):

The Neolithic Hungarians are close to Sardinians (this has been replicated in study after study, so it's no longer a surprise when you find Neolithic Europeans that look like Sardinians).

What is surprising is that one KO1 Neolithic European is with the hunter-gatherers (top of the plot). At some level you would expect to find some hunter-gatherers in the earliest Neolithic communities in Europe as Europe wasn't empty land when the early farmers showed up. And KO1 appears one of those guys, "caught in the act" of first contact between the two groups.

The two Bronze Age samples are more like modern continental Europeans but not exactly like modern Hungarians. The Iron Age sample is in the no-man's land between Europe and the Caucasus and his "Asian" Y chromosome and mtDNA seems to agree that this is no ordinary European.

UPDATE III (How they looked):

I really like the visualization of hair and eye color predictions of the last two columns of the table on the right. It seems that the ancient Hungarians had mainly brown hair with more variability after 5,000 years ago. They mostly had brown eyes except three individuals.

An interesting thing is that NE7 who seems to have light hair and blue eyes is just like other Sardinian-like farmers of the Neolithic and also has the mtDNA haplogroup N1a1a1a that is ultra-typical for Neolithic people from Europe. So this is a warning not to conflate appearance with ancestry.

UPDATE IV (Y chromosomes):

As always, the supplement has many of the interesting details. Two Neolithic males were C6 which is the same "weird" haplogroup that La Brana hunter-gatherer from Spain had. Two other ones were I2a which is what Loschbour and Swedish hunter-gatherers had. Strangely, no Neolithic males had G which was found before in many Neolithic Europeans.

A new finding is that the Bronze Age individual BR2 belonged to haplogroup J2a1. I think this is the first time this has been found in ancient DNA and it falsifies the Phoenician sea-faring theory of the dispersal of this lineage.

Finally, the Iron Age Hungarian belonged to haplogroup N. I believe this was found in ancient Magyars from Hungary before, but apparently it existed there long before them.

Nature Communications 5, Article number: 5257 doi:10.1038/ncomms6257

Genome flux and stasis in a five millennium transect of European prehistory

Cristina Gamba et al.

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.

Link

Y chromosomes and mtDNA of early farmers from Hungary

A new preprint has just appeared on the bioRxiv. It's free to read so I'll just summarize some results. First:

The haplotype of the Mesolithic skeleton from the Croatian Island Korčula belongs to the mtDNA haplogroup U5b2a5 (Dataset S3). The sub-haplogroup U5b has been shown to be frequent in pre-Neolithic hunter-gatherer communities across Europe [28–30,32,33,45,46]. 

But:

Contrary to the low mtDNA diversity reported from hunter-gatherers of Central/North Europe [28–30], we identify substantially higher variability in early farming communities of the Carpathian Basin  including the haplogroups N1a, T1, T2, J, K, H, HV, V, W, X, U2, U3, U4, and U5a (Table 1). Previous studies have shown that haplogroups N1a, T2, J, K, HV, V, W and X are most characteristic for the Central European LBK and have described these haplogroups as the mitochondrial ʻNeolithic packageʼ that had reached Central Europe in the 6th millennium BC [36,37]. Interestingly, most of these haplogroups show comparable frequencies between the STA, LBKT and LBK,

N1a is the "signature group" of the LBK based on previous publications and now it seems that it was also found in the Starcevo culture of Hungary. The mtDNA PCA plot (right) shows clearly that the Hungarian farmers are very similar to the German ones so it seems that the LBK is a direct outgrowth of the Carpathian Neolithic; some earlier models of "demic diffusion" argued that Neolithic farmers spread slowly across Europe, picking up hunter-gatherer ancestry as they went along, but now it seems that at least in the Hungary->Germany part of this journey interaction with hunter-gatherers was minimum.

mtDNA change over time in Europe is pictured in Figure 3 (left) showing a shared haplotype analysis. The Y-chromosome data genetic distance is shown on the right and shows the Balkan-Anatolian-Caucasian-Mesopotamian relationship of the early farmer Y-chromosomes. Practically, this is due to haplogroup G2a (and especially G2a2b), which has turned up in lots of ancient European farmers (including the famous Iceman):

Three STA individuals belong to the NRY haplogroup F* (M89) and two specimens can be assigned to the G2a2b (S126) haplogroup, and one each to G2a (P15) and I2a1 (P37.2) (Dataset S3, S5). The two investigated LBKT samples carry haplogroups G2a2b (S126) and I1 (M253). Furthermore, the incomplete SNP profiles of eight specimens potentially belong to the same haplogroups; STA: three G2a2b (S126), two G2a (P15), and one I (M170); LBKT: one G2a2b (S126) and one F* (M89) (Dataset S5).

I believe this is the first ancient finding of haplogroup I1 which attains a peak in modern Swedes. This might be useful to those who have tied this to Germanic migrations because of this, as it was already in Central Europe with the earliest farmers.

Interestingly:

Surprisingly, Y chromosome haplogroups, such as E1b1b1 (M35), E1b1b1a1 (M78), E1b1b1b2a (M123), J2 (M172), J1 (M267), and R1b1a2 (M269), which were claimed to be associated with the Neolithic expansion [23–25], have not been found so far in the 6th millennium BC of the Carpathian Basin and Central Europe. Intriguingly, R1a and R1b, which represent the most frequent European Y chromosome haplogroups today, have been reported from cultures that emerged in Central Europe during the 3rd/2nd millennium BC, while a basal R type has been reported from a Palaeolithic sample in Siberia [60] in agreement with a proposed Central Asian/Siberian origin of this lineage. In contrast, G2a has not been detected yet in late Neolithic cultures [42,43]. This suggests further demographic events in later Neolithic or post-Neolithic periods.

A cautionary tale against over-reliance on modern distributions to trace ancient origins.

Also:

Considering the entire set of 32 published NRY records available for Neolithic Europe thus far, the low paternal diversity is indeed quite remarkable: G2a is the prevailing haplogroup in the Central European and Carpathian Basin Neolithic, and in French and Iberian Neolithic datasets [36,40,41]. There are only two exceptions, namely one E1b1b (V13) [41] individual from the Avellaner cave in Spain (~5,000-4,500 BC), and two I2a [40] individuals from Treilles, France (~3,000 BC).

biorxiv http://dx.doi.org/10.1101/008664

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Anna Szécsényi-Nagy et al.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early farming south-eastern European and Carpathian Basin cultures on Central European populations of the 6th-4th millennium BC. Our comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through south-eastern Europe and the Carpathian Basin into Central Europe. Our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting patrilineal descent system and patrilocal residential rules among the early farmers.

Link

EAA 2013 abstracts

The bioarchaeology of the neolithic Carpathian Basin

By the beginning of the 6th Millennium cal BC, the first farmers reached the Carpathian Basinwhere the last transition to food production and sedentary life took place. The early neolithic groups became restructured both in their cultural and genetic composition in the 6th and 5th Millennium BC, affected by at least five major Northern Balkan impulses. The western part of the area became a major communication zone, mediating between South Eastern and Central Europe. Our working group has been focusing on this early population history of Eastern Hungary and of Transdanubia, developing and comparing ancient DNA, stable isotope, osteological and archaeological data gained from not less than 600 neolithic skeletons (6000–4300 cal BC).  

In the session we would like to give an account of the DNA and stable isotope (SR, N, C) analysis, carried out within the frames of a three-year interdisciplinary project funded by the German Research Foundation along with the co-evaluation of these results with osteology and zooarchaeology, as well as giving a comparative interpretation of this data within our present socioarchaeological knowledge.

The megalithic past of the Bronze Age kurgans of the North Pontic Region 

The Early Bronze Age (EBA) burial mounds (kurgans) in the western part of the North Pontic Region (NPR) display a tendency to be erected over earlier megalithic ritual constructions. The initial purpose of these megalithic structures might have been cosmology-related. In succeeding time periods the initial astronomic purpose could have been forgotten and these megalithic sites became designated at sacred places suited for distinguished burials. Megalithic elements comprising the initial constructions became incorporated into the subsequent burials. The Revova kurgan from western NPR is one such construction. It was erected over a megalithic structure in a shape of a tortoise with the stone elements of the construction being astronomically aligned. An assembly of disarticulated human remains deposited in the center of the construction dated to the Eneolithic (4200 BC). On the other hand, the layout of stones comprising the “Tortoise” appears to most accurately line up with the movement of celestial objects as they appeared on the sky around 6300 BC. Mitochondrial DNA lineage extracted from the remains was characteristic to the Mesolithic/Neolithic hunter-gatherer populations from northern Europe as well as Bronze Age groups from south Siberia. 

The spread of domestic pig in the central and Eastern part of the Romanian territory described by the ancient mithochondrial DNA

Previous genetic analysis showed the presence of two different haplotypes for domestic pigs from 11 different sites in the South-Eastern part of Romania: the Near-Eastern haplotype ANC-Y1-5A, for 18 individuals, and ANC-Aside european haplotype, for 8 individuals. This study reveals the genetic signature for other 52 samples (5000–3500 BC, from 7 archaeologic sites) covering the central and Eastern parts of Romania. After the DNA extraction, PCR, and sequencing, no ANC-Aside haplotype was found, but, apart from the Near-Eastern ANC-Y1-5A haplotype, identified in the majority of domestic pig samples, the european ANC-Cside haplotype (generally identified in the wild boars), was also found in three domestic pigs from Poduri, Ghigoiesti and Trusesti. The wide spread of the wild boar with the ANC-Cside haplotype not only on the entire Romanian territory, but also, as previously shown, in it’s close proximity, and the emergence of this genetic signature in both wild and domestic pigs from three different sites could support the idea of a local domestication of the wild boar after 4500 BC, in this specific area.

The genetic make-up of the Linear Pottery culture

The Linear Pottery culture (LBK) is one of the first Central European Neolithic farming cultures marking the transition from a hunter-gatherer to a farming lifestyle. The LBK is thought to have originated from Early Neolithic cultures in the Carpathian Basin from where it extended across Europe over a vast distribution area spanning from the River Rhine to the Ukraine. Consequently, its role during the process of Neolithisation in Central Europe is subject of a long-standing debate in archaeology, anthropology and human genetics. Ancient DNA studies have provided direct insights into Mesolithic and Neolithic mitochondrial diversity indicating genetic discontinuity between Central Europe’s autochthonous hunter-gatherers and LBK populations. Comprehensive population genetic analyses utilizing large databases of present-day populations have disclosed genetic affinities of the LBK to the modern-day Near East, Anatolia and the Caucasus, supporting genetic influx from this region into Central Europe at the advent of farming and explaining the apparent genetic discontinuity between foragers and farmers. We will summarize the inferences that have been drawn from 108 LBK data to provide an overview of genetic diversity of the first farming communities in Central Europe, which represents an invaluable genetic perspective for the discussion of the Neolithic in the Carpathian Basin.

Bell Beaker child burials and their gender identity in the light of DNA analysis

The DNA analysis of 53 child burials from the Bell Beaker cemetery at Hostice-I produced data on 21 sexed individuals. Out of 14 burials with male gender attributes were 12 individuals biologically male and two determinate as women. Cases of girls that were brought up as boys probably existed in 3rd Millennium BC burial customs. Out of seven children buried in the female position only 1 was actually biological female (juvenile 15–20 years) and 6 male (2 juvenile 15–19/20 years). That means four boys (aged 3–4, 7, 8–12, 15) were in fact buried as women. Such a result is in line with known demographic unbalance within Beaker cemeteries. Most young girls were not buried at the communal cemetery and considerable number of boys were buried in the female fashion. This is rather high number of cases when the masculine attributes were downplayed in the burial customs and it is hard to interpret whether they were boys supposed to be brought up as women or they had yet no right to act as men, unlike some other sub-adult boys, perhaps members of families with ascribed hereditary warrior status. It almost seems that some young boys were socially considered to be girls, perhaps until ceremonial rite of passage, social initiation of some kind.

Ancient Human DNA – A problem of interpretation

The problem with ancient human DNA is not contamination with modern human DNA any more. This still happens, but aDNA scientists can now recognise it and deal with it. The problem is with the overinterpretation of results. Only a few mitochondrial and Y chromosome aDNA sequences may be obtained from a burial assemblage, but these are interpreted in a population genetics framework which incorporates DNA sequences obtained from present day populations. This type of analysis ignores the possibility that social structures can affect genetic outcomes, as is seen in traditional societies and has recently been recognised by evolutionary geneticists. Societies practising patrilocal exogamy versus endogamy have been studied and the mtDNA and Y chromosomal haplotype diversity analysed. Patrilocal societies show high mtDNA diversity while Y haplotype diversity is reduced. Endogamous societies do not show the reduction in Y diversity, but mtDNA diversity is maintained. Ancient DNA results from several Neolithic sites can therefore be interpreted to identify the type of social structure present. Patrilocal exogamy is the most parsimonious interpretation and this is corroborated by Sr isotope studies from LBK sites.

 Ancient DNA discloses multiple migrations into Central Europe during the Neolithic

The Central European Neolithic is characterised by a succession of differentiated archaeological cultures indicating a period of fundamental cultural change. A recurrent question in archaeology and anthropology is whether cultural change in prehistory was accompanied by variation in the gene pool of associated populations. Ancient DNA studies based on mitochondrial DNA revealed a discontinuity between Central Europe’s autochthonous hunter-gatherers and their early farmers and between the latter and the present-day population, suggesting further migration events after the initial Neolithisation. However, to date little attention has been drawn to cultural and potentially population changes in subsequent Neolithic periods. To investigate this issue, we conducted a large chronological study including a succession of nine cultures from the Mittelelbe-Saale region, Saxony-Anhalt, Germany to reconstruct a detailed temporal profile of cultural and genetic diversity in Central Europe. The presented diachronic study spans overall 3,950 years from the beginning of the Neolithic period and the introduction of producing subsistence strategies ~5,500 BC to the appearance of structured chiefdoms in the Early Bronze Age ~2,200–1,550 BC. This transect through time identified multiple population dynamic events during the Neolithic, which involved genetic influx from various regions in Europe.

 Ancient DNA and isotope analysis of the Starčevo graves at Alsónyék-Bátaszék

Between 2006 and 2009 at Alsónyék-Bátaszék a settlement with 26 graves of the Starčevo culture were unearthed. More than 400 various features belonged to this early Neolithic period on an extension of 80 hectares. The archaeological findings underline the significance of Alsónyék-Bátaszék, which is to date the largest Starčevo site uncovered in present-day Hungary. We analysed the 26 Starčevo burials from Alsónyék from ancient DNA and stable isotopic aspects, involving them in our three-year bioarchaeological Neolithic project. The excellent DNA preservation made it possible to gain reproduced mitochondrial DNA results from all skeletons, and we could additionally type the Y chromosome in 5 of the male individuals. The strontium (87Sr/86Sr) and oxygen (δ18Op) isotopic data obtained an insight into the mobility and kinship system of the population. The carbon (δ13C) and nitrogen (δ15N) isotope analyses of the skeletons supported a basis for a diet reconstruction, supplementing the archaeozoological proceedings of the site. Our results from the Alsónyék-Bátaszék Starčevo specimens, dated between ca. 5800-5500 cal BC, denote a milestone of the early Neolithic bioarchaeological studies in Transdanubia.

 6–5th millennium BC cultural changes in Western Hungary tested by ancient DNA

Western Hungary (Transdanubia) was one of the key regions at the process of Neolithisation in Central Europe. The Starcevo culture, representing the earliest farmers on this region, settled down at latest 5750 cal BC south of the Lake Balaton. It had a major role in the formation of the Linearbandkeramik culture in Transdanubia. The following Sopot, Lengyel cultures of the late Neolithic and Early Copper Age Transdanubia show repeated cultural influences from the Balkan, besides local extant cultural traditions. 

The focus of our study is the process of these cultural changes in Transdanubia, in the view of ancient DNA, investigating mitochondrial and Y chromosomal lineages and markers. A total of 292 skeletons were sampled and processed, with an overall success rate of 89% for mitochondrial DNA. Comparing the mitochondrial and Y chromosomal results with other published data and evaluating them with population genetic analyses, we gained a peerless insight into the population history of Western Hungary. 

Our study may give an additional help to prehistoric archaeology, for a better understanding of the nature of cultural changes, supporting it with a new type of evidence, in order to see Transdanubia as a mediating area between South East and Central Europe.

Diverse occupants of Hungarian kurgan

Antiquity Volume: 86 Number: 334 Page: 1097–1111

Immigration and transhumance in the Early Bronze Age Carpathian Basin: the occupants of a kurgan

Claudia Gerling

You never know until you look. The authors deconstruct a kurgan burial mound in the Great Hungarian Plain designated to the Yamnaya culture, to find it was actually shared by a number of different peoples. The Yamnaya were an influential immigrant group of the Late Copper Age/Early Bronze Age transition. The burials, already characterised by their grave goods, were radiocarbon dated and further examined using stable isotope analysis on the human teeth. The revealing sequence began with a young person of likely local origin buried around or even before the late fourth millennium BC—a few centuries before the arrival of the Yamnaya. It ended around 500 years later with a group of different immigrants, apparently from the eastern mountains. These are explained as contacts built up between the mountains and the plain through the practice of transhumance.

Link

Mediterranean ornaments in the Hungarian Neolithic

The use of Spondylus ornaments by European Neolithic cultures is well known, and is one of the characteristics tracking the spread of the Neolithic into Europe. A new study has looked at late Neolithic Hungary, to track the origin of these ornaments, confirming that they did indeed come from the Mediterranean (Adriatic or Aegean), and not the Black Sea or fossil shells from the Carpathian Basin.

Given the evidence that late Neolithic European farmers, even as far north as Sweden were indeed of Mediterranean origin, their continued use of these ornaments possibly reflects a tradition going back to their origins in the Aegean, rather than simply a fashion that spread simply for its decorative properties.

Journal of Archaeological Science, doi:10.1016/j.jas.2012.09.022

Tracing the source of Late Neolithic Spondylus shell ornaments by stable isotope geochemistry and cathodoluminescence microscopy

Bernadett Bajnoczi et al.

Determination of the source of Spondylus objects is essential for the interpretation of Late Neolithic exchange systems and the social role of shell ornaments. We performed stable isotope analysis combined with cathodoluminescence microscopy study on ornaments (beads, bracelets) made of Spondylus shells excavated at the Aszod-Papi foldek archaeological site in Hungary, to define their origin. For comparison Spondylus finds from Neolithic sites of Greece, modern Spondylus shells from the Aegean and the Adriatic, as well as fossil Spondylus and Ostrea shells from the Carpathian Basin were also examined. Oxygen isotope composition of Spondylus finds from Aszod ranges between -1.9 and 2.1 ‰ and overlaps with the oxygen isotope range of shell objects from other Neolithic sites. Modern Spondylus shells from the Aegean and the Adriatic show overlapping δ18O values with one another and with the Neolithic objects; while recent shells of the Black Sea clearly are separate isotopically from the Mediterranean ones and most of archaeological artefacts. Spondylus shells from the Aszod site have Mediterranean origin; their source can be the Aegean or the Adriatic. Based on a former strontium isotope study the use of fossil Spondylus shells is excluded as raw material used for ornaments, however, in recent years the use of fossil shells was reintroduced. The shell ornaments from Aszod-Papi foldek and the fossil oyster shells collected from the Carpathian Basin exhibit some overlapping oxygen isotope values; however, cathodoluminescence microscopy indicates that the Spondylus objects retained their original aragonite material. Diagenetic calcite, which occurs typically in the fossil shells, was not detected in the ornaments suggesting that the studied objects were made of recent shells. Calcitic parts observed in some Spondylus objects are not related to fossilisation.

Link

A look at Y chromosomes of Romania via Count Dracula

In short: researchers tried to see whether they could identify a specific Y chromosome lineage associated with the House of Basarab in Romania, the most famous member of which is Vlad the Impaler, an inspiration for the mythical Count Dracula. To do this, they tested Basarab-surnamed individuals, as well as the general Romanian population.

The whole exercise was, in a sense, a failure, since it neither disclosed a Basarab-specific lineage, nor resolved the historical question about the origin of the House of Basarab (Vlach or Cuman). But, it gave us some wonderful new data on Romania that is, of course, quite welcome.

This seems like a good candidate for a future ancient DNA study, assuming of course, that Vlad and his family are still in their final resting place, and there are brave enough researchers to disturb them (j/k).

On a more serious note, the authors correctly state that even if the Basarab house was originally Turkic, they could still have carried West Eurasian chromosomes, since incoming Turkic groups in Europe were not purely Mongoloid like their more remote ancestors. On the other hand, I note that most of the Basarab-surnamed individuals belonged to E-V13, I-P37.2, J-M241 all of which are almost certainly native Romanian. If one of them carries the original chromosome, then the odds are in favor of a Romanian origin, although nothing short of ancient DNA work can resolve the issue, assuming that's possible.

Table S1 contains the new Romanian data, and Table S2 data from surrounding populations (Hungary, Bulgaria, Ukraine).

PLoS ONE 7(7): e41803. doi:10.1371/journal.pone.0041803

Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings

Begoña Martinez-Cruz et al.

Vlad III The Impaler, also known as Dracula, descended from the dynasty of Basarab, the first rulers of independent Wallachia, in present Romania. Whether this dynasty is of Cuman (an admixed Turkic people that reached Wallachia from the East in the 11th century) or of local Romanian (Vlach) origin is debated among historians. Earlier studies have demonstrated the value of investigating the Y chromosome of men bearing a historical name, in order to identify their genetic origin. We sampled 29 Romanian men carrying the surname Basarab, in addition to four Romanian populations (from counties Dolj, N = 38; Mehedinti, N = 11; Cluj, N = 50; and Brasov, N = 50), and compared the data with the surrounding populations. We typed 131 SNPs and 19 STRs in the non-recombinant part of the Y-chromosome in all the individuals. We computed a PCA to situate the Basarab individuals in the context of Romania and its neighboring populations. Different Y-chromosome haplogroups were found within the individuals bearing the Basarab name. All haplogroups are common in Romania and other Central and Eastern European populations. In a PCA, the Basarab group clusters within other Romanian populations. We found several clusters of Basarab individuals having a common ancestor within the period of the last 600 years. The diversity of haplogroups found shows that not all individuals carrying the surname Basarab can be direct biological descendants of the Basarab dynasty. The absence of Eastern Asian lineages in the Basarab men can be interpreted as a lack of evidence for a Cuman origin of the Basarab dynasty, although it cannot be positively ruled out. It can be therefore concluded that the Basarab dynasty was successful in spreading its name beyond the spread of its genes.

Link

Not Neolithic after all (?)

I did not read these, but it appears that the case for East Eurasian mDNA in Neolithic Hungary may in fact be suspect.

‘Early Neolithic’ graves of the Carpathian Basin are in fact 6000 years younger—Appeal for real interdisciplinarity between archaeology and ancient DNA research Eszter Bánffy, Guido Brandt and Kurt W Alt J Hum Genet advance online publication, June 7, 2012; doi:10.1038/jhg.2012.36 Full Text

Response to Data on Hungarian Early Neolithic graves by Bánffy et al Tamas Zeke and Zsuzsanna Guba J Hum Genet advance online publication, June 7, 2012; doi:10.1038/jhg.2012.64 Full Text

Unexpected ancient mtDNA from Neolithic Hungary

This seems like a tie-in to another recent post on Neolithic and Bronze Age Ukraine. I don't think even a science fiction writer could have predicted the kinds of ancient DNA results we are getting from Europe. We have genetic discontinuity between Paleolithic and Neolithic, and between Neolithic and present, and, apparently, discontinuity between Neolithic cultures themselves, and wholly unexpected links to East Asia all the way to Central Europe.

When faced with data such as this, one can only say: what the hell happened during European prehistory?

UPDATE (8 Jun 2012): The age of these remains has been questioned.

Journal of Human Genetics advance online publication 15 September 2011; doi: 10.1038/jhg.2011.103

HVS-I polymorphism screening of ancient human mitochondrial DNA provides evidence for N9a discontinuity and East Asian haplogroups in the Neolithic Hungary

Zsuzsanna Guba et al.

Analysis of mitochondrial mutations in the HVS-I region is an effective method for ancient human populational studies. Discontinuous haplotype data between the first farmers and contemporary Europeans has been described before. Our contribution is based on a survey initiated on the Neolithic skeletons from Hungarian archaeological sites in the Alföld. This Lowland, the Hungarian Plain, is well excavated as an important region for spread of Neolithic culture from Near East and Balkans toward Central and Western Europe, started circa 8000 years ago. HVS-I sequences from nt15977 to nt16430 of 11 such specimens with sufficient mitochondrial DNA preservation among an extended Neolithic collection were analysed for polymorphisms, identifying 23 different ones. After assigning all single-nucleotide polymorphisms, a novel, N9a, N1a, C5, D1/G1a, M/R24 haplogroups were determined. On mitochondrial control mutations at nt16257 and nt16261, polymorphic PCRs were carried out to assess their distribution in remains. Neolithic data set was compared with contemporary Vác samples and references, resulting in higher frequency of N9a in Alföld as a remarkable genetic discontinuity. Our investigation is the first to study mutations form Neolithic of Hungary, resulting in an outcome of Far Eastern haplogroups in the Carpathian Basin. It is worth further investigation as a non-descendant theory, instead of a continuous population history, supporting genetic gaps between ancient and recent human populations.

Link

Scarcity of lactase persistence in medieval Hungarians

The interesting finding of this paper is not so much the fact that conquering Magyars (who came from the east) lacked the common European allele for lactase persistence, but rather that the common folk largely did as well: there were only two individuals homozygous for the derived (persistent) allele, and one heterozygous one.

This is quite unexpected, as present-day Hungarians have noticeable lactase persistence (pdf; Yuval Itan et al., A worldwide correlation of lactase persistence phenotype and genotypes). The origin of lactase persistence in Europeans had been dated to no earlier than the onset of the Neolithic, as it was absent in early Neolithic Central Europeans, as well as northern European hunter-gatherers.

A scenario in which most of the selection for LP occurred over the last millennium is quite difficult to believe, and this would imply that there was an influx of LP-folk into the Hungarian population to account for its present-day frequency. We urgently need data on other contemporaneous European population to determine whether they had LP frequencies similar to the present-day ones or not.

My guess is that these 10th-11th century Hungarians comprised, in accordance to what physical anthropology suggests, a mix of Mongoloid and Caucasoid types of eastern origin, both of which are expected to be low on LP, while present-day Hungarians are largely descended from pre- and post-Hungarian Central European Caucasoids who possessed the regular (for central Europeans) high LP frequency.

Am J Phys Anthropol DOI: 10.1002/ajpa.21490

Comparison of lactase persistence polymorphism in ancient and present-day Hungarian populations

Dóra Nagy et al.

The prevalence of adult-type hypolactasia varies ethnically and geographically among populations. A C/T–13910 single nucleotide polymorphism (SNP) upstream of the lactase gene is known to be associated with lactase non-persistence in Europeans. The aim of this study was to determine the prevalence of lactase persistent and non-persistent genotypes in current Hungarian-speaking populations and in ancient bone samples of classical conquerors and commoners from the 10th–11th centuries from the Carpathian basin; 181 present-day Hungarian, 65 present-day Sekler, and 23 ancient samples were successfully genotyped for the C/T-13910 SNP by the dCAPS PCR-RFLP method. Additional mitochondrial DNA testing was also carried out. In ancient Hungarians, the T-13910 allele was present only in 11% of the population, and exclusively in commoners of European mitochondrial haplogroups who may have been of pre-Hungarian indigenous ancestry. This is despite animal domestication and dairy products having been introduced into the Carpathian basin early in the Neolithic Age. This anomaly may be explained by the Hungarian use of fermented milk products, their greater consumption of ruminant meat than milk, cultural differences, or by their having other lactase-regulating genetic polymorphisms than C/T-13910. The low prevalence of lactase persistence provides additional information on the Asian origin of Hungarians. Present-day Hungarians have been assimilated with the surrounding European populations, since they do not differ significantly from the neighboring populations in their possession of mtDNA and C/T-13910 variants.

Link

Y chromosomes of Vlax Roma

From the paper:

The Gypsies arrived in Europe 900–1100 years ago, when they first appeared in the Balkans. The present-day Gypsy population groups in Europe are the compound product of the early migrations from the Balkans into Europe [1]. The Gypsies came to Hungary from the Balkans in two large migrations. The Carpathian Romanies arrived in the 15th century and the Vlax Romanies came in the 19th century. The Carpathian Gypsies speak Hungarian and the Vlax Romanies speak Hungarian and Romani languages.

Interesting:

A median-joining (MJ) network of haplogroup H1a-M82 has demonstrated the sharing of identical Indian specific Y-chromosomal lineages between all Romani populations including Malaysian Indians as well as the Vlax Romanies (Fig. 2A and B). This common lineage of haplogroup H1a-M82 represents a common descent from a single ancestor providing a strong genetic link to the ancestral geographical origin of the proto-Gypsies [1]. According to Sengupta et al. [24] the age of microsatellite variation within haplogroup H1 in Indian populations is more than 9.7 +/- 4.4 ky. This time was estimated to be 992 years (95%CI 425–3472) in the Romani populations investigated by Gresham et al. [1] suggesting the Indian H1 haplogroup is the ancestral one.

Gresham et al. (pdf) used the genealogical mutation rate. Hence, the discrepancy between the Sengupta et al. age estimates and their own is partly due to the choice of mutation rate. Nonetheless, it's obvious that the Balkan H1 is still 3 times younger than the Indian one, and obviously of South Asian origin. Notice also how the Gresham et al. paper gives a large confidence interval for its estimate, in agreement with my observations about the inadequacy of a limited number of Y-STRs, and Y-STRs in general to couple tightly with historical events.

Nonetheless, if one uses an order-of-magnitude approach, the Gresham et al. estimate is quite compatible with historical knowledge about the arrival of Gypsy founders to the Balkans, just as was the case for Serbian Roma.

The ~1ky estimate for Balkan Gypsy H1 is similar to the ~1ky estimate for the updated J1 Cohen Modal Haplotype. For reasons explained in that post, this is probably an overestimate, and I can envision a scenario according to which the tribal descendants of an H1-man who lived in the 1st millennium AD made their way to Europe at the turn of the millennium, proliferating into the Gypsy communities of today.

Related:

• Y-chromosome study of Serbian Roma
• Y chromosomes of Iberian Gypsies
• Y chromosomes of Bayash Romani
• Y-chromosomes of Albanian populations (Ferri et al. 2010)

Forensic Science International: Genetics doi:10.1016/j.fsigen.2010.08.017

Paternal genetic history of the Vlax Roma

Andrea Zalán et al.

Romanies constitute the largest minority group belonging to different subgroups in Hungary. Vlax Romanies are one of these Romani subgroups. The Gypsies came to Hungary from the Balkans in two large migrations. The Carpathian Romanies arrived in the 15th century and the Vlax Romanies came in the 19th century. The Carpathian Gypsies speak Hungarian and the Vlax Romanies speak Hungarian and Romani languages.
Only a limited number of genetic studies of Y-chromosomal haplotypes/haplogroups have been done before, moreover most studies did not contain information regarding the investigated Roma populations which subgroups belong to.
In the present study, we analyzed a wide set of Y-chromosomal markers to do comparable studies of the Vlax Roma in eastern Hungarian regions. The results can be compared in the context of previously published data on other Romani groups, Indian and Hungarian reference populations.
Haplogroups H1a-M82 and J2a2-M67 were most common in the investigated population groups. A median-joining network of haplogroup H1a-M82 has demonstrated the sharing of identical Indian specific Y-chromosomal lineages between all Romani populations including Malaysian Indians as well as the Vlax Romanies. This common lineage of haplogroup H1a-M82 represents a common descent from a single ancestor provides a strong genetic link to the ancestral geographical origin of the proto-Gypsies.
The detected haplogroups in the Vlax Romani population groups can be classified into two different Y-chromosomal lineages based on their putative origin. These lineages include ancestral Indian (H1a-M82), present-day Eurasian (J2a2-M67, J2*-M172, E1b1b1a-M78, I1-M253, R1a1-M198 and R1b1-P25) Y-chromosome lineages. Presence of these lineages in the paternal gene pool of the Roma people is illustrative of the Gypsy migration route from India through the Balkan to the Carpathian Basin.

Avar and Hungarian horses were different

Genetica. 2009 Sep 30. [Epub ahead of print]

Mitochondrial sequence variation in ancient horses from the Carpathian Basin and possible modern relatives.

Priskin K, Szabó K, Tömöry G, Bogácsi-Szabó E, Csányi B, Eördögh R, Downes CS, Raskó I.

Movements of human populations leave their traces in the genetic makeup of the areas affected; the same applies to the horses that move with their owners This study is concerned with the mitochondrial control region genotypes of 31 archaeological horse remains, excavated from pre-conquest Avar and post-conquest Hungarian burial sites in the Carpathian Basin dating from the sixth to the tenth century. To investigate relationships to other ancient and recent breeds, modern Hucul and Akhal Teke samples were also collected, and mtDNA control region (CR) sequences from 76 breeds representing 921 individual specimens were combined with our sequence data. Phylogenetic relationships among horse mtDNA CR haplotypes were estimated using both genetic distance and the non-dichotomous network method. Both methods indicated a separation between horses of the Avars and the Hungarians. Our results show that the ethnic changes induced by the Hungarian Conquest were accompanied by a corresponding change in the stables of the Carpathian Basin.

Link

History of the people of the Hungarian plain in the 1st millennium

Hum Biol. 2008 Dec;80(6):655-67

History of the peoples of the Great Hungarian Plain in the first millennium: a craniometric point of view

Holló G, Szathmáry L, Marcsik A, Barta Z.

We carried out an examination relying on six dimensions of 1,573 crania coming from the Great Hungarian Plain. The crania represent seven archeological periods: Sarmatian age (1-4th century), the period of transition (about 400-420), Hun and Gepidic epochs (about 420-455 and 455-567, respectively), early Avar age (about 568-670), late Avar period (about 670-895), the epoch of the Hungarian conquest and settlement (about 895-1000), and the Arpadian age (about 1000-1301). We were curious about the anatomical background behind cultural changes of the various populations that inhabited this area. After having noticed some discontinuities between the populations, as revealed by univariate analysis of single dimensions, we performed a principal-components analysis to see whether or not the diverse components showed eventual breaks in the sequence of the populations. Knowing that all the dominant populations had Asian roots, except for the Gepids of Germanic origin, we expected a considerable difference between the Gepidic population and all the other inhabitants. We also assumed that a conquest itself with a large-scale assimilation was unlikely to leave breaklike traits in anatomical patterns, except for aggressive conquests. We found that the second principal component (which correlated with cranial breadth and partly with height) showed a remarkable hiatus in both sexes between Gepids and early Avars. Having done a statistical proof (simultaneous tests for general linear hypotheses) of the observed phenomenon, we found that the gap referring to subsequent populations was significant only in males. A possible reason for this result is that the Avar conquest was much more radical than has been thought. In addition, considering that men were more likely to die in wars, women survived and were assimilated into the conquerors' populations with higher probability, so it is not surprising that the results of multicomparison tests are significant only in men.

Link

Central European farmers not descended from local hunter-gatherers (Bramanti et al. 2009)

This is the real power of DNA: the topic of whether central European farmers were the result of demic diffusion from the southeast or indigenous hunter-gatherers who adopted the agricultural economy has been endlessly debated in archaeological circles.

We are finally in a position to give an answer to the question, and the answer is in favor of the diffusionist camp and against the idea of acculturation by local hunter-gatherers. Surprisingly, modern Central Europeans do not appear to be a simple hunter-gatherer/farmer mix, suggesting that even later events (post-Neolithic) have shaped their genetic diversity.

This study is also a powerful argument against the idea of genetic continuity across long time spans. Most ancient DNA studies so far have reached a similar conclusion. Thus, it also destroys the supposed justification for continuity from Paleolithic Europe to modern times that early mtDNA work (of the Daughters of Eve variety) has proposed, hand in hand with the hunter acculturation hypothesis.

The paper is covered in National Geographic:

Central and western Europe's first farmers weren't crafty, native hunter-gatherers who gradually gave up their spears for seeds, a new study says.

Instead, they were experienced outsiders who arrived on the scene around 5500 B.C. with animals in tow—and the locals apparently didn't roll out the welcome wagon.

"Within a few generations, all the farmers—probably coming from southeast Europe—moved into central Europe bringing their culture, [livestock], and everything," Joachim Burger, a molecular archaeologist at the University of Mainz in Germany, said via email.

The finding is based on analysis of genetic material in the skeletal remains of ancient hunter-gatherers and early farmers found in Germany, Lithuania, Poland, and Russia—though farming is thought to have reached areas as far west as western France during the period of rapid expansion, about 7,500 years ago.

The study goes against a long-standing idea that Europe's first farmers were former hunter-gatherer populations that had settled the region after the last ice age, about 10,000 years ago.

Perhaps, the thinking went, the hunter-gatherers had observed farming practices during their travels or had learned from neighbors.

Instead, the researchers found, the hunter-gatherers and the early farmers remained segregated, according to the study, to be published tomorrow in the journal Science.

And the press release:

Analysis of ancient DNA from skeletons suggests that Europe's first farmers were not the descendants of the people who settled the area after the retreat of the ice sheets. Instead, the early farmers probably migrated into major areas of central and eastern Europe about 7,500 years ago, bringing domesticated plants and animals with them, says Barbara Bramanti from Mainz University in Germany and colleagues. The researchers analyzed DNA from hunter-gatherer and early farmer burials, and compared those to each other and to the DNA of modern Europeans. They conclude that there is little evidence of a direct genetic link between the hunter-gatherers and the early farmers, and 82 percent of the types of mtDNA found in the hunter-gatherers are relatively rare in central Europeans today.

For more than a century archaeologists, anthropologists, linguists, and more recently, geneticists, have argued about who the ancestors of Europeans living today were. We know that people lived in Europe before and after the last big ice age and managed to survive by hunting and gathering. We also know that farming spread into Europe from the Near East over the last 9,000 years, thereby increasing the amount of food that can be produced by as much as 100-fold. But the extent to which modern Europeans are descended from either of those two groups has eluded scientists despite many attempts to answer this question.

Now, a team from Mainz University in Germany, together with researchers from UCL (University College London) and Cambridge, have found that the first farmers in central and northern Europe could not have been the descendents of the hunter-gatherers that came before them. But what is even more surprising, they also found that modern Europeans couldn't solely be the descendents of either the hunter-gatherer alone, or the first farmers alone, and are unlikely to be a mixture of just those two groups. "This is really odd", said Professor Mark Thomas, a population geneticist at UCL and co-author of the study. "For more than a century the debate has centered around how much we are the descendents of European hunter-gatherers and how much we are the descendents of Europe's early farmers. For the first time we are now able to directly compare the genes of these Stone Age Europeans, and what we find is that some DNA types just aren't there - despite being common in Europeans today."

Humans arrived in Europe 45,000 years ago and replaced the Neandertals. From that period on, European hunter-gatherers experienced lots of climatic changes, including the last Ice Age. After the end of the Ice Age, some 11,000 years ago, the hunter-gatherer lifestyle survived for a couple of thousand years but was then gradually replaced by agriculture. The question was whether this change in lifestyle from hunter-gatherer to farmer was brought to Europe by new people, or whether only the idea of farming spread. The new results from the Mainz-led team seems to solve much of this long standing debate.

"Our analysis shows that there is no direct continuity between hunter-gatherers and farmers in Central Europe," says Prof Joachim Burger. "As the hunter-gatherers were there first, the farmers must have immigrated into the area."

The study identifies the Carpathian Basin as the origin for early Central European farmers. "It seems that farmers of the Linearbandkeramik culture immigrated from what is modern day Hungary around 7,500 years ago into Central Europe, initially without mixing with local hunter gatherers," says Barbara Bramanti, first author of the study. "This is surprising, because there were cultural contacts between the locals and the immigrants, but, it appears, no genetic exchange of women."

The new study confirms what Joachim Burger´s team showed in 2005; that the first farmers were not the direct ancestors of modern European. Burger says "We are still searching for those remaining components of modern European ancestry. European hunter-gatherers and early farmers alone are not enough. But new ancient DNA data from later periods in European prehistory may shed also light on this in the future."

And from archaeology.about.com:

A new study published by Barbara Bramanti and colleagues in Science Express on September 4, 2009, supports what some scholars have suspected all along—that the LBK likely were an in-migration of people from the Balkans, and that they did not, initially anyway, do much mixing at all with the earlier inhabitants of Europe.

Bramanti and her colleagues compared the mitochondrial DNA from 20 central European Upper Paleolithic, Mesolithic and Neolithic hunter-gatherers to that from 25 Neolithic farmers and 484 modern Europeans, spanning an age range from about 13,400 to 2,300 BC. The data shows that the early farmers and hunter-gatherers were from distinctively different populations.

This paper follows up on and to a degree contradicts with the hypothesis of an earlier paper that looked only at mtDA of the Neolithic farmers. That study (Haak et al. 2005) discovered that the farmers had a distinctive difference between the current residents of Europe, and hypothesized that that meant that the hunter-gatherers might have been more like the modern inhabitants, and thus, the LBK would have been only a minor component.

The earlier paper by Haak et al. they refer to.

(More technical details once I read the full paper)

UPDATE:

Pre-farming populations seem to have been dominated by mtDNA haplogroup U:

it is intriguing to note that 82% of our 22 hunter-gatherer individuals carried clade U (fourteen U5, two U4, and two unspecified U-types; table 1).

The hunter-gatherers had no N1a -which was a signature of early farmers in the Haak et al. paper- or of haplogroup H, the most common mtDNA haplogroup in Europeans today. The only non-U types in hunter-gatherers were all from the Ostorf site and included haplogroups T2e, J, and K.

The farmers:

In a previous study, we showed that the early farmers of Central Europe carried mainly N1a, but also H, HV, J, K, T, V, and U3 types (11, 12). We found no U5 or U4 types in that early farmer sample.

UPDATE I:

It is important to note the implications of this study: the most certain conclusion is that Neolithic farmers in Central Europe are very sharply differentiated from the Paleolithic-Mesolithic populations. This is clear evidence in favor of the diffusionist idea, since the acculturation hypothesis predicts that the mtDNA of the early farmers would be roughly that of the pre-farming population that picked up the new technology.

However, the evidence of this paper also contradicts the plain demic diffusion hypothesis. According to this hypothesis, farmer genes are gradually replaced by hunter genes as the farming economy spreads, because in each step there is a mix of farmer-indigenous populations which go on to colonize regions beyond the frontier. This is not what appears to have happened. Rather, it seems the farmers moved across Europe with very little interaction with pre-farmers. A long period of no contact between the LBK and foragers is actually supported by archaeology. I have termed this type of diffusion the "skipping stone":

In the Skipping Stone model, farmers move out in search of new territories before they have started to blend with the local foragers; the genetic impact of the initiators of the movement is preserved.

The great speed of the Linearbandkeramik farmers was also experienced by farmers who spread across the Mediterranean. The spread of agriculture in Europe does not appear to have been a slow process of interaction between farmer and forager, but rather a blitz by the first farmers, followed later, after the spread had already occurred by admixture with some of the foragers that remained.

We must also be certain not to jump into conclusions about the relative contributions of farmer and forager in the modern gene pool. Clearly both the idea of a predominantly "Paleolithic" and a predominantly "Neolithic" gene pool is problematic; such continuity is not really evident. However, the reasons for the discontinuity up to the present may be manifold: e.g., later population movements into Europe, or natural selection changing the gene pool without subsequent change of population.

What we do know is this: first farmers were not local foragers who abandoned the old ways for the new ones. Amalgamation between farmer and forager did not happen quickly as the farming economy spread. Finally it did happen, of course, and either because (i) there were few foragers in the mix, or (ii) their mtDNA was selected against, modern central Europeans have very little mitochondrial descent from the earliest European populations.

PS: Natural selection against forager mtDNA is not very outlandish. For example, a severe reduction of U5a1 and U5b haplogroup in Britain from ancient to modern times has been observed, which could potentially mark another data point in a process of selection against that haplogroup over time.

My personal guess is that both demography and selection may have played a role in the marginalization of hunter-gatherer mtDNA . LBK farmers were already 3 thousand years removed from the earliest agriculturalists of the Near East, so it is conceivable that they had evolved an mtDNA gene pool adapted to the new lifestyle that outcompeted the indigenous European one. But, the long period of isolation from foragers may mean that only farmer mtDNA benefited from the demographic boom associated with the new economy, and by the time relations between the two groups warmed up, the relatively few newcomers already dwarfed the older population demographically.

UPDATE II (Sep 4):

To understand the magnitude of the difference between farmers and hunter-gatherers, the authors calculate their Fst=0.163, which can be compared with a maximum value of 0.0327 among modern Europeans and 0.133 for modern Eurasians from Europe to Australia. Subsequently, the authors test the hypotheses of (a) continuity between hunter-gatherers and farmers, and (b) continuity between hunter-gatherers and modern Central Europeans, rejecting both.

This isn't very surprising in the light of the anthropological evidence in favor of diffusion of farmers from the Near East and against the acculturation hypothesis presented recently by Pinhasi et al. The very close relationship of the LBK skulls and their proximity to samples from Nea Nikomedeia in Greece and Catal Hoyuk in Anatolia contrasts with the Mesolithic populations.

UPDATE III (Sep 21):

Some possible anthropological evidence for post-LBK infusion into Central Europe:

Mesolithic Europeans display considerable variation in humero-clavicular and brachial indices yet none approach the extreme "hyper-polar" morphology of LBK humans from the MESV. In contrast, Late Neolithic and Early Bronze Age peoples display elongated brachial and crural indices reminiscent of terminal Pleistocene and "tropically adapted" recent humans. These marked morphological changes likely reflect exogenous immigration during the terminal Fourth millennium cal BC.

Science doi:10.1126/science.1176869

Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe’s First Farmers

B. Bramanti et al.

Following the domestication of animals and crops in the Near East some 11,000 years ago, farming reached much of Central Europe by 7,500 years before present. The extent to which these early European farmers were immigrants, or descendants of resident hunter-gatherers who had adopted farming, has been widely debated. We compare new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers, and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in Central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into Central Europe at the onset of the Neolithic.

Link

Forensic study of Hungarian Y-chromosomes

My tabulation of the haplogroup composition is in the figure. The last four haplogroups that aren't very visible occur at a frequency of 0.9, 0.5, 0.5, 0.5% respectively. Nothing too surprising about these results, except for the H1 which probably represents the Gypsy element, and R2 which may be both of South Asian Gypsy or Central Asian/Siberian origin. The lone example of haplogroup N, which was found in 2 of 4 ancient Magyars confirms the low genetic influence of the original Magyars on present-day Hungarians.

It is also fairly interesting that comparatively, Bulgarians end up as being closest to Hungarians, with a negative Fst value. Perhaps this represents some commonality of an Asian element added to a Balcano-Danubian population. Non-significant differences (above 5% level) were also observed in comparison to Romanians, Slovenians, Ukrainians, and surprisingly Norwegians, perhaps due to the fairly unusual high R1a/R1b mix in both populations.

Forensic Sci Int Genet. 2009 Mar;3(2):e27-8.

Hungarian population data for 11 Y-STR and 49 Y-SNP markers.

Völgyi A, Zalán A, Szvetnik E, Pamjav H.

49 Y-chromosomal single nucleotide polymorphisms (SNPs) with TaqMan assay and 11 Y-chromosomal STR loci were tested in 215 independent Hungarian male samples. Genetic distances to 23 other populations were calculated based on haplogroup frequencies with AMOVA implemented in Arlequin2.0. Based on distances phylogenetic tree was constructed with Neighbor-joining method using Phylip 3.66. Haplotype and haplogroup diversity values were calculated.

Link

Magyars and Madjars

American Journal of Physical Anthropology doi:10.1002/ajpa.20984

A Y-chromosomal comparison of the Madjars (Kazakhstan) and the Magyars (Hungary)

A.Z. Bíró et al.

Abstract

The Madjars are a previously unstudied population from Kazakhstan who practice a form of local exogamy in which wives are brought in from neighboring tribes, but husbands are not, so the paternal lineages remain genetically isolated within the population. Their name bears a striking resemblance to the Magyars who have inhabited Hungary for over a millennium, but whose previous history is poorly understood. We have now carried out a genetic analysis of the population structure and relationships of the Madjars, and in particular have sought to test whether or not they show a genetic link with the Magyars. We concentrated on paternal lineages because of their isolation within the Madjars and sampled males representing all extant male lineages unrelated for more than eight generations (n = 45) in the Torgay area of Kazakhstan. The Madjars show evidence of extensive genetic drift, with 24/45 carrying the same 12-STR haplotype within haplogroup G. Genetic distances based on haplogroup frequencies were used to compare the Madjars with 37 other populations and showed that they were closest to the Hungarian population rather than their geographical neighbors. Although this finding could result from chance, it is striking and suggests that there could have been genetic contact between the ancestors of the Madjars and Magyars, and thus that modern Hungarians may trace their ancestry to Central Asia, instead of the Eastern Uralic region as previously thought.

Link

Y chromosomes of Hungarians

I had blogged about this research in 2005 when it was presented in the ESHG conference. Now there is a full article in Annals of Human Genetics. See also my post on Ancient Hungarian mtDNA. An interesting bit from the paper:

Haplogroup I was detected with almost equal frequency in the two modern populations: 24% in Hungarians and 21.7% in Szeklers. However, two of its major subclades- I1a-M253 and I1b*(xM26) – show an opposite occurrence in the two ethnic groups, 8% and 13%, respectively, in Hungarians, and 16.5% and 5.2% in Szeklers. These are within the range of normal central and eastern European values (Rootsi et al., 2004; Peričić et al., 2005). The elevated frequency of Hg I1a together with higher frequency of R1b-M269 in Szekler population might be the consequence, at least in part, of the genetic impact of people of German origin, who settled in Transylvania from the 12th century onwards (Transylvanian Saxons)(Makkai, 1990; Kristó, 2002).

Also:

The J1-M267 Y-chromosomal lineage is notably frequent in Szeklers (10.3%; a value far above the range for other central and eastern European populations (Semino et al., 2000a, 2004; Di Giacomo et al., 2004), while its frequency in Hungarians (3.0%) is unremarkable.

...

Among these J2-M172 subclades, J2e1-M102 is more frequent in Szeklers (7.2%) than in Hungarians (4.0%), while the undifferentiated J2-M172* Y chromosomes are slightly more common in Hungarian population (8% vs. 3.1%). Both J2f*-M67 and J2f1-M92 lineages were detected in our study in one single individual, in each population.

Interestingly, the two ancient indiviuals harboring Y-haplogroup N3 (anc21 and anc28) were also classified anthropologically as Europo-Mongolid, while anc21 harbored the Caucasoid mtDNA haplogroup H. This is consistent with the notion that the Mongoloid elements in ancient Hungarians fused with Caucasoid elements, although the results from the modern population suggests that the blend was finally overwhelmed by the Caucasoid component.

Annals of Human Genetics doi:10.1111/j.1469-1809.2008.00440.x

Y-Chromosome Analysis of Ancient Hungarian and Two Modern Hungarian-Speaking Populations from the Carpathian Basin

B. Csányi et al.

The Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic family. The Tat C allele is an interesting marker in the Finno-Ugric context, distributed in all the Finno-Ugric-speaking populations, except for Hungarians. This question arises whether the ancestral Hungarians, who settled in the Carpathian Basin, harbored this polymorphism or not. 100 men from modern Hungary, 97 Szeklers (a Hungarian-speaking population from Transylvania), and 4 archaeologically Hungarian bone samples from the 10^th century were studied for this polymorphism. Among the modern individuals, only one Szekler carries the Tat C allele, whereas out of the four skeletal remains, two possess the allele. The latter finding, even allowing for the low sample number, appears to indicate a Siberian lineage of the invading Hungarians, which later has largely disappeared.

The two modern Hungarian-speaking populations, based on 22 Y-chromosomal binary markers, share similar components described for other Europeans, except for the presence of the haplogroup P*(xM173) in Szekler samples, which may reflect a Central Asian connection, and high frequency of haplogroup J in both Szeklers and Hungarians. MDS analysis based on haplogroup frequency values, confirms that modern Hungarian and Szekler populations are genetically closely related, and similar to populations from Central Europe and the Balkans.

Link