Bronze Age Plague

This paper used the same data as the Allentoft et al. paper, but instead of focusing on the human DNA recovered from ancient Eurasians, it went looking for interesting stuff in the non-human DNA (the stuff that is usually thrown away).

The result: 2,800-5,000 year old Yersinia pestis from Europe to the Altai. It will be cool to look at even older remains than the Bronze Age, but this already pushes the date for plague by a couple thousand years, and implicates steppe people in its earliest spread.

Cell Volume 163, Issue 3, p571–582, 22 October 2015

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

Simon Rasmussen18, Morten Erik Allentoft18, Kasper Nielsen, Ludovic Orlando, Martin Sikora, Karl-Göran Sjögren, Anders Gorm Pedersen, Mikkel Schubert, Alex Van Dam, Christian Moliin Outzen Kapel, Henrik Bjørn Nielsen, Søren Brunak, Pavel Avetisyan, Andrey Epimakhov, Mikhail Viktorovich Khalyapin, Artak Gnuni, Aivar Kriiska, Irena Lasak, Mait Metspalu, Vyacheslav Moiseyev, Andrei Gromov, Dalia Pokutta, Lehti Saag, Liivi Varul, Levon Yepiskoposyan, Thomas Sicheritz-Pontén, Robert A. Foley, Marta Mirazón Lahr, Rasmus Nielsen, Kristian Kristiansen, Eske Willerslev

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

Link

Into, out of, and across the Eurasian steppe

A new paper in Nature adds to the earlier study in the same journal by presenting data from 101 ancient Eurasians. The year is not yet halfway over, but it seems that the ancient DNA field is moving towards a new norm of studying dozens of individuals at a time and comprehensively tackling the "big problems" that have vexed archaeologists, linguists, and historians for decades if not centuries.

The first conclusion of the new study is the detection of the migration from the steppe to Europe that was the title piece of the earlier study. The authors do not present quantitative estimates of the amount of demographic replacement effected by the Yamnaya-to-Corded Ware migration, so it will be interesting to see if there are any minor significant differences in these. But, the two papers have different Yamnaya and Corded Ware samples, and yet arrive at qualitatively similar conclusions, so at least this part of the story should be considered firmly "settled".

The second conclusion is the migration from the European steppe to the Afanasievo culture of the Altai. This has been long-hypothesized based on the physical type of the Afanasievo people and their possession of a similar pastoralist/wheeled vehicle toolkit that would have allowed them to cover the huge difference between Europe and the Altai. This confirms movement #2 of the Anthony/Ringe model, although I doubt that this migration had anything to do with Tocharians as detailed below. But, it did happen.

The third conclusion is that the later steppe cultures of the Sintashta and Andronovo (putative Indo-Iranians according to some), were not a continuation of the Yamnaya-Afanasievo people, but had extra Neolithic farmer ancestry. So, it seems that Neolithic farmers entered the steppe, and the development of steppe cultures did not happen in isolation. Whether this involved migration of Corded Ware people (as the authors prefer), who were already a mixture of Yamnaya and Neolithic farmers, or some other mixture of Neolithic farmers with steppe populations (e.g., Tripolye plus Yamnaya) remains to be seen.

The fourth conclusion of the paper is that these steppe cultures were also later replaced by people of at least partial East Asian or "Native American"-like ancestry.  So, it seems that movements into the steppe happened both on the western end (as the incursion of Neolithic farmer ancestry into the Sintashta proves), but also on the eastern end, with the Europeoid populations of western origin receiving admixture from the eastern periphery of the Eurasian steppe.

As for the Yamnaya, the authors do not find a very strong signal of admixture (as did the earlier study), which they attribute quite plausibly to the lack of eastern hunter-gatherers in their dataset. On the other hand, they claim that the "Caucasus" genetic component in the steppe populations was of steppe ancestry rather than Near Eastern/Caucasian origin as was claimed in the earlier paper. This is based on the statistic D(Yoruba, Armenia BA; Yamnaya, Corded Ware) that is not significantly different from zero. However, Corded Ware is a mixture of Yamnaya and European Neolithic, so the sign of this statistic is determined by the sign of the statistic D(Yoruba, Armenia BA; Yamnaya, European Neolithic). If Yamnaya was simply a steppe population, descendants of local people without ancestry from the Middle East/Caucasus, then this statistic would be positive because of the shared Middle Eastern ancestry of Armenia BA and European Neolithic. Whereas, if Yamnaya is a mixture of a steppe population and a Middle Eastern/Caucasian one, then the statistic would be positive/negative for the respective parts, which would be consistent with an average not different from zero. I am sure that when the new data is re-analyzed together with the eastern hunter-gatherers it will be clear that the Yamnaya are not a pure steppe population.

Nonetheless, I am quite glad to read a sentence such as this:

Populations in northern and central Europe were composed of a mixture of the earlier hunter-gatherer and Neolithic farmer10 groups, but received ‘Caucasian’ genetic input at the onset of the Bronze Age (Fig. 2).

It seems that my prediction the the West_Asian component would appear in post-5ka Europeans and was related to Indo-Europeans has been adequately confirmed by the last two papers.

Speaking of the Caucasus/Middle East, it seems clear as a first approximation that the Bronze Age Armenians are quite similar to modern Armenians. Whether the genetic continuity of Armenians extends beyond the Bronze Age, or Armenians were formed by mixture in the Bronze Age remains to be seen. The question of Armenian linguistic origins is of course separate as it is commonly understood that the Armenian language is unrelated to Anatolian languages and may have arrived in Armenia from the Balkans at around the Bronze Age-Iron Age transition.

The authors also study some phenotypic traits such as lactase peristence (Yamnaya had some, but overall prevalence was much lower than modern Europeans, hence lots of selection to the present), and skin eye pigmentation. Like Wilde et al., and Mathieson et al., the steppe populations seem to have had brown eyes. Given that so did Neolithic Europeans, and (presumably) ancient Middle Easterners/Caucasians, I think it's a good bet that Proto-Indo-Europeans (whatever solution to the PIE urheimat one accepts) were a brown-eyed people, or in the very least far from the blue-eyed "Aryans" of racial mythology. Even the Bronze Age and Iron Age Asians seem to have been a predominantly brown-eyed people, although the derived HERC2 allele seems to be at a higher frequency in them than in the steppe Europeans.

The story of the Y-chromosomes seems very interesting, although these are not resolved to fine detail. The most interesting aspect of this part of the work is the appearance of haplogroup J in Iron Age samples from Russia, Armenia, and the Altai. This may tie in to the question of the Tocharian origins, which I have claimed were associated with R1b, rather than R1a (as the Indo-Iranians were). The modern Uygurs (who are partially of Tocharian origin) have both J2 and R1b, so were the recipients of West Eurasian elements other than the R1a that so seem to have dominated the eastern steppe, including the Afanasievo. I continue to think there's no evidence that the Afanasievo is Proto-Tocharian, as it's in the wrong place and 3,000 years before the attestation of Tocharian. 

Overall this is an amazing study which adds a lot to what we know about Bronze Age Eurasia. Hopefully there is more to come in the second half of 2015, but for the time being there is plenty to chew on.

Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Population genomics of Bronze Age Eurasia

Morten E. Allentoft, Martin Sikora, Karl-Göran Sjögren, Simon Rasmussen, Morten Rasmussen, Jesper Stenderup, Peter B. Damgaard, Hannes Schroeder, Torbjörn Ahlström, Lasse Vinner, Anna-Sapfo Malaspinas, Ashot Margaryan, Tom Higham, David Chivall, Niels Lynnerup, Lise Harvig, Justyna Baron, Philippe Della Casa, Paweł Dąbrowski, Paul R. Duffy, Alexander V. Ebel, Andrey Epimakhov, Karin Frei, Mirosław Furmanek, Tomasz Gralak, Andrey Gromov, Stanisław Gronkiewicz, Gisela Grupe, Tamás Hajdu, Radosław Jarysz, Valeri Khartanovich, Alexandr Khokhlov, Viktória Kiss, Jan Kolář, Aivar Kriiska, Irena Lasak, Cristina Longhi, George McGlynn, Algimantas Merkevicius, Inga Merkyte, Mait Metspalu, Ruzan Mkrtchyan, Vyacheslav Moiseyev, László Paja, György Pálfi, Dalia Pokutta, Łukasz Pospieszny, T. Douglas Price, Lehti Saag, Mikhail Sablin, Natalia Shishlina, Václav Smrčka, Vasilii I. Soenov, Vajk Szeverényi, Gusztáv Tóth, Synaru V. Trifanova, Liivi Varul, Magdolna Vicze, Levon Yepiskoposyan, Vladislav Zhitenev, Ludovic Orlando, Thomas Sicheritz-Pontén, Søren Brunak, Rasmus Nielsen, Kristian Kristiansen & Eske Willerslev

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Link

101 ancient genomes from Bronze Age Eurasia

New data has been posted online. This seems related to this earlier post. Hopefully the study linked to this data will appear soon, but genome bloggers can get to it thanks to the early data release.

Investigation of Bronze Age in Eurasia by sequencing from 101 ancient human remains. 

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.

Link

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

Dairy farming transition ~2,500 years BC in the far north of Europe

Proceedings of the Royal Society B doi: 10.1098/rspb.2014.0819

Neolithic dairy farming at the extreme of agriculture in northern Europe

Lucy J. E. Cramp et al.

The conventional ‘Neolithic package’ comprised animals and plants originally domesticated in the Near East. As farming spread on a generally northwest trajectory across Europe, early pastoralists would have been faced with the challenge of making farming viable in regions in which the organisms were poorly adapted to providing optimal yields or even surviving. Hence, it has long been debated whether Neolithic economies were ever established at the modern limits of agriculture. Here, we examine food residues in pottery, testing a hypothesis that Neolithic farming was practiced beyond the 60th parallel north. Our findings, based on diagnostic biomarker lipids and δ13C values of preserved fatty acids, reveal a transition at ca 2500 BC from the exploitation of aquatic organisms to processing of ruminant products, specifically milk, confirming farming was practiced at high latitudes. Combining this with genetic, environmental and archaeological information, we demonstrate the origins of dairying probably accompanied an incoming, genetically distinct, population successfully establishing this new subsistence ‘package’.

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