Natural selection and ancient European DNA

A new preprint on the bioRxiv studies the same data as the recent Haak et al. paper, but focuses on natural selection in Europe. Until recently, selection could only be studied by looking at modern populations, but since selection is genetic change over time effected by the environment, it's possible that studies like this will be the norm in the future.

The new study seems to confirm the results of Wilde et al. on steppe groups, as the Yamnaya had a very low frequency of the HERC2 derived "blue eye" allele and a lower frequency of the SLC45A2 "light skin" allele than any modern Europeans. The Yamnaya seem to have been fixed for the other SLC24A5 "light skin" allele which seems to have been at high frequency in all ancient groups save the "Western Hunter Gatherers".

It seems that light pigmentation traits had already existed in pre-Indo-European Europeans (both farmers and hunter-gatherers) and so long-standing philological attempts to correlate them with the arrival of light-pigmented Indo-Europeans from the steppe (or indeed anywhere), and to contrast them with darker pre-Indo-European inhabitants of Europe were misguided. If anything, it seems that the "fairest of them all" were the Scandinavian hunter-gatherers, and a combination of light/dark pigmentation was also present in Neolithic farmers and Western Hunter Gatherers in various combinations.

It also seems that both the theory that lactose tolerance started with LBK farmers and the theory that it came to Europe from milk-drinking steppe Indo-Europeans were wrong, as this trait seems to be altogether absent in European hunter-gatherers, farmers, and Yamnaya, and make a very timid appearance in the Late neolithic/Bronze Age before shooting up in frequency to the present.

Another new development is the ability to predict "genetic height" from ancient DNA. I think this may be a little bit superfluous as you can predict "actual height" by measuring long bone lengths. On the other hand, actualized height depends not only on genetics but also on diet, disease, etc., so it's useful to look at genetic changes in such polygenic traits directly.

A big surprise was the presence of the derived EDAR allele in Swedish hunter-gatherers. This allele is very rare in modern Europeans and seems to have pleiotropic effects in East Asians. This raises the question why this allele (that was so successful in East Asians), never "took hold" in Europeans. One possibility is that it never provided an advantage to Europeans (I don't think anyone really knows what it's actually good for). Another is that Swedish hunter-gatherers simply didn't contribute much ancestry to modern Europeans and so the allele never got the chance to rise in frequency by much.

bioRxiv http://dx.doi.org/10.1101/016477

Eight thousand years of natural selection in Europe

Iain Mathieson et al.

The arrival of farming in Europe beginning around 8,500 years ago required adaptation to new environments, pathogens, diets, and social organizations. While evidence of natural selection can be revealed by studying patterns of genetic variation in present-day people, these pattern are only indirect echoes of past events, and provide little information about where and when selection occurred. Ancient DNA makes it possible to examine populations as they were before, during and after adaptation events, and thus to reveal the tempo and mode of selection. Here we report the first genome-wide scan for selection using ancient DNA, based on 83 human samples from Holocene Europe analyzed at over 300,000 positions. We find five genome-wide signals of selection, at loci associated with diet and pigmentation. Surprisingly in light of suggestions of selection on immune traits associated with the advent of agriculture and denser living conditions, we find no strong sweeps associated with immunological phenotypes. We also report a scan for selection for complex traits, and find two signals of selection on height: for short stature in Iberia after the arrival of agriculture, and for tall stature on the Pontic-Caspian steppe earlier than 5,000 years ago. A surprise is that in Scandinavian hunter-gatherers living around 8,000 years ago, there is a high frequency of the derived allele at the EDAR gene that is the strongest known signal of selection in East Asians and that is thought to have arisen in East Asia. These results document the power of ancient DNA to reveal features of past adaptation that could not be understood from analyses of present-day people.

Link (pdf)

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

mtDNA from Chalcolithic Iberia (El Mirador cave)

A very exciting new study from Chalcolithic Iberia. The authors compare their mtDNA data with those from the Brandt et al. (2013) paper which includes German samples from the same time.

The following plot seems quite useful. From its caption:

This study: El Mirador (MIR). Published prehistoric cultures [21]: Hunter-gatherer central (HGC), Linear Pottery culture (LBK), Rössen culture (RSC), Schöningen group (SCG), Baalberge culture (BAC), Salzmünde culture (SMC), Bernburg culture (BEC), Corded Ware culture (CWC), Bell Beaker culture (BBC), Unetice culture (UC), Funnel Beaker culture (FBC), Pitted Ware culture (PWC), Hunter-Gatherer south (HGS), (Epi) Cardial (CAR), Neolithic Portugal (NPO), Neolithic Basque Country and Navarre (NBQ), Treilles culture (TRE), Hunter-gatherer east (HGE), Bronze Age Siberia (BAS), Bronze Age Kazakhstan (BAK).

From the paper:

In none of the analyses El Mirador sample shows close genetic affinities with a contemporaneous Bell Beaker population of 29 specimens gathered from three sites in Germany. The Bell Beaker mtDNA signal is characterized by high frequencies (around 50%) of H haplogroup that in El Mirador only reaches 26%. This heterogeneity in the genetic composition of geographically close populations adds further complexity to future reconstructions of these ancient expansions and correlates with the existence of contemporaneous groups with and without the typical Bell Beaker burial kit.

mtDNA may not be the best tool for studying the spread of Bell Beakers (if this involved men), but this shows that the high frequency of H in Bell Beakers of Germany (observed by Brandt et al.) is not due to an even higher frequency of H in Iberia.

PLoS ONE 9(8): e105105. doi:10.1371/journal.pone.0105105

Mitochondrial DNA from El Mirador Cave (Atapuerca, Spain) Reveals the Heterogeneity of Chalcolithic Populations

Daniel Gómez-Sánchez,Iñigo Olalde et al.

Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

Link

Ancient central European mtDNA across time (Brandt, Haak et al. and Bollongino et al.)

Two important new papers appeared in Science today. In the first one (Brandt, Haak et al.), researchers compiled mtDNA results from 364 prehistoric central Europeans from the early Neolithic to the early Bronze Age, spanning about four millennia of history. Importantly they uncover not a smooth transition between early Neolithic farmers and modern Europeans, but a punctuated series of haplogroup frequency changes that cannot really be explained by genetic drift in a single European population evolving over time. Hopefully this kind of research can be repeated in other parts of the world, as it provides a way to see evolution and migration as it happens.

Earlier work has disproved the hypothesis that modern Europeans are simply "acculturated" hunter-gatherers, and this newer research disproves the idea that they are simply the descendants of early farmers, little modified since the beginning of the Neolithic.

I am sure that myself and others will spend some time trying to digest the wealth of information present in the paper and its supplementary materials. Yet, one conclusion can already be made, that migrationism is alive and well. Anyone adhering to a "pots not people" paradigm will find difficult to explain the sharp discontinuities found in the genetic record. European foragers contrast with the earliest farmers, who, in turn, contrast with and the Late Neolithic copper cultures that supplanted them a few thousand years later and spawned the Bronze Age world. If pots aren't people, it's strange that archaeological cultures defined largely by pots (right) also appear to mark genetic contrasts.

These discontinuities are most evident in Figure 3 from the paper:

You may follow the grey line to see how central Europe, once populated exclusively by hunter-gatherers, experienced a virtual disappearance of their matrilineages for almost two thousand years after the advent of farming.  Then, between the Middle to Late Neolithic, around five thousand year ago, the hunter-gatherers make their re-appearance before their lineages converge to their modern (minority) frequency. The authors present a model of migration to explain these events, illustrated in a movie in the supplementary material, and also in the figure on the left.

Of particular interest is a set of haplogroups marked by the yellow line (I, U2, T1, R) and are most strongly represented in the Unetice and Corded Ware samples before reverting to a small minority in the present-day. These may be potentially very informative to understand the c. 5,000-year old ago upheaval. I reproduce below three of the genetic distance maps from the supplement for the three latest cultures (CWC: Corded Ware; BBC: Bell Beaker; and UC: Unetice):

I note the European-ness of Bell Beaker (probably due to elevated frequencies of haplogroup H) and the eastern European-ness/west Asian-ness of Corded Ware/Unetice.

Moving on to the next shorter paper by Bollongino et al. which produces evidence for an interesting hypothesis: that hunter-gatherers did not disappear in central Europe after the introduction of farming, but some of their descendants persisted for at least two thousand years afterwards:

In summary, the results of 14C and stable isotope analysis, together with the DNA evidence, suggest that the Blätterhöhle individuals are sampled from three distinct populations: (i) Mesolithic hunter-gatherers, (ii) Neolithic farmers, and (iii) Neolithic fisher-hunter-gatherers (special-izing in freshwater fish). The latter two notably date to the fourth mil-lennium BC, which is around 2000 years after the introduction of farming to Central Europe.

I was reminded of an older paper about first contact between farmers and hunter-gatherers. An important consequence of the second paper is that hunter-gatherer lineages in modern Europeans may have come not only from outlying areas where foragers persisted in greater numbers, but also from within the farming realm itself.

Science 11 October 2013: Vol. 342 no. 6155 pp. 257-261 DOI: 10.1126/science.1241844

Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity 

Guido Brandt, Wolfgang Haak et al.

The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.

Link

Science DOI: 10.1126/science.1245049

2000 Years of Parallel Societies in Stone Age Central Europe

Ruth Bollongino et al.

Debate on the ancestry of Europeans centers on the interplay between Mesolithic foragers and Neolithic farmers. Foragers are generally believed to have disappeared shortly after the arrival of agriculture. To investigate the relation between foragers and farmers, we examined Mesolithic and Neolithic samples from the Blätterhöhle site. Mesolithic mitochondrial DNA sequences were typical of European foragers, whereas the Neolithic sample included additional lineages that are associated with early farmers. However, isotope analyses separate the Neolithic sample into two groups: one with an agriculturalist diet and one with a forager and freshwater fish diet, the latter carrying mitochondrial DNA sequences typical of Mesolithic hunter-gatherers. This indicates that the descendants of Mesolithic people maintained a foraging lifestyle in Central Europe for more than 2000 years after the arrival of farming societies.

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.