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

Afanasievo, Okunev, Andronovo, Sintashta DNA?

A reader alerts me to this article in Russian, but you can use Google Translate to get the gist of it. Some interesting bits (note that "pit"=Yamna):

I can not ignore the question I now have is particularly exciting - the origin of the Indo-Europeans. Community Indo-Europeists animatedly discussing just appeared as a preprint work of David Raika and his colleagues discovered by studying the genomes of people Neolithic and Bronze Age that a decisive influence on the genetic landscape of Europe has had a migration of people pit culture to the north and west in the middle of the III millennium. BC .e. As a result, according to geneticists, there was a population associated with the Corded Ware culture, and from it are the origin of the later Indo-European. By the same conclusions about the same time came the other team's leading geneticists led by Eske Villerslevom.
...

A steppe, we thought had long been a special world, and differs sharply from the Middle East, and from the European. Migration from there - so it seemed - were mainly directed not to the west and to the east, along the steppes, in the direction of Central Asia, which the ancient Indo-Europeans, Afanasiev media culture (descendants of the people of the pit culture or their ancestors steppe) reached no later turn IV- III millennium BC. It is now confirmed and the group Villersleva.
...

By the way, it also happens that paleoanthropologists prompted geneticists way of research - and turned out to be right. As it happens, for example, with native Okunevskaya culture of South Siberia. When 20 years ago, we found that craniologically (by a combination of traditional measurement and we proposed new informative features of the structure of the cranial sutures and holes) okunevtsy - "cousins" of American Indians, few believed us. Firstly, in okunevtsah ever seen Caucasoid-Mongoloid Métis like the Kazakhs, and secondly, the ancestors of the Indians withdrew from Siberia to the New World at least 10 thousand. Before the Yenisey there Okunevskaya culture.

Eske Willerslev Now and his colleagues have fully confirmed our conclusion. They confirmed the close relationship between the carriers and the pit Afanasiev cultures and migration ancestors sintashtintsev and Andronov from Europe in the Urals and further to Siberia - but this is already a long time, few archaeologists and anthropologists doubted.

I hope more details will appear soon on what promises to be a very interesting new study. The author seems to be referring to his theory of a relationship between Okunev and Amerindians, and I'm wondering if this is simply "Ancient North Eurasian" ancestry or an even more specific link. Any Russian readers who can dig up more information are invited to post in the comments.