Breakdown - 'Population Genomics Of Stone Age Eurasia' Paper

New Genetics Results Covering The Mesolithic-Neolithic Transition

A major new paper dropped this week, a pre-print with researchers from a wide range of countries and institutions including Allentoft and Willerslev, both dominant figures in the field of ancient genetics. Allentoft et al 2015 was a huge intervention in the archaeological zeitgeist which I’ve written about before. This time he has delivered another substantial piece of work - over 1600 genomes dating across the Mesolithic-Neolithic transition, from Britain to Lake Baikal, combined with radiocarbon dating, stable isotope analysis and pollen records. This is a massive undertaking that must have taken years to put together.

So what are the highlights of this paper?

1. Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia

2. Newly identified genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists

3. The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this “Great Divide”, including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east.

4. The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000 years.

5. Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries

6. Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.

So lets unpick these six points:

Hunter-Gatherer Diversity & Divergence

The Last Glacial Maximum (LGM) was roughly 22kya in Europe. At this point Upper Palaeolithic peoples were pushed into ‘refugia’ zones, along with all the plants, insects, animals and other life which would recolonise Europe after the ice retreated. As the glaciers melted, humans surged back into central and northern Europe, these populations then formed the ‘post-glacial’ foragers of the Mesolithic.

The results of this paper indicate the following:

• The central importance of a Caucasian Upper Palaeolithic population (25k BP) to both post-glacial foragers and Anatolian farmers. (mixture of West Eurasian HGs and Basal Eurasians)

• Three major clusters of post-glacial populations: Italian, Ukranian & Russian

  • All the Danish forager genomes originated from the Italian population and remained a homogeneous population for 5,000 years

  • Swedish Mesolithic foragers derived 60% of their ancestry from the Ukrainian population - moving in a southeast to Baltic corridor

  • Northern Scandinavia populated by Russian foragers

• Iberian Mesolithic population initially related to Italian sources, but later Iberians contained between 30-40% Ukrainian sources, suggesting westward expansion

• Late Mesolithic Swedish groups show higher Italian derived ancestry, indicating either migration from Danish sources or a later wave from southern Europe

• Ukrainian hunter-gatherers themselves show an influx from southern Italian foragers, meaning a possible later expansion from southern to eastern Europe

• Finally - several genomes from the Middle Don region show early mixing with Caucasian derived populations, roughly 20-30% as far back as 7,300 BP

In conclusion then, the results for post-glacial Europe reveal a complex picture of recolonisation and secondary migrations. Curiously the Solutrean/Magdalenian populations of Iberia don’t seem prominent in the post-glacial era, which may just be a product of genetic interpretation. More investigations needed there.

A New Hunter-Gatherer Group?

The final result in the previous section - the early Caucus mixing with Ukrainian foragers - is a significant result. The individuals in question come from the Golubaya Krinitsa burial ground, which itself is part of a wider Dnepr ceramic using hunter-gatherer cluster. The graves belong to the ‘ Mariupol-type’ - BUT - only this group of mixed Caucasian/Ukrainian foragers serve as the majority ancestors to the Yamnaya steppe peoples.

This is a fascinating result. Only one mixed population of foragers went on to become the ancestral pool for the steppe invaders of Europe. The remaining Ukrainian hunter-gatherers don’t seem to have contributed to the formation of steppe peoples.

The ‘Great Divide’

While we know that the Neolithisation of Europe was a major event in world history, previous studies have not been able to resolve the geographic differences of this migration at scale. Here we see a truly profound event, which the authors dub ‘The Great Divide’

Running from the Baltic to the Black Sea is a dividing line in European genetics. The Neolithic Anatolian or Early European Farmers which entered Europe through the Aegean came to replace the vast majority of foragers west of this dividing line.

No such replacement occurred in the east.

“The arrival of Anatolian-related ancestry in different regions spans an extensive time period of over 3,000 years… On the eastern side of this divide, no ancestry shifts can be observed during this period. In the East Baltic region, Ukraine and Western Russia local hunter-gatherer ancestry prevails until ~5,000 BP without noticeable input of Neolithic Anatolian-related farmer ancestry. This Eastern genetic continuity is in remarkable congruence with the archaeological record showing persistence of pottery-using hunter-gatherer-fisher groups in this wide region, and delayed introduction of cultivation and husbandry by several thousand years”

Why does this matter?

This result demonstrates that from the Neolithic onwards, Europe would be deeply divergent in its population history and demographics. Culturally, linguistically, genetically, economically - Europe was divided down this line by the coming of the Neolithic farmers.

Western Ancestral Shifts

As previously reported, populations to the west of the line mixed and were replaced by the Anatolian EEF farmers, most populations were no more than 10% hunter-gatherer. A resurgence in hunter-gatherer ancestry in various places, in particular the Danish Pitted Ware cluster included two ~5,000-year-old Danish male individuals, composed entirely of Swedish hunter-gatherer ancestry. The detailed work combining strontium isotopes with the genetics shows one of the men to be non-local.

Neolithic populations themselves in the mid to late era were regionally split, with a southern to western migratory corridor and a central-eastern-Scandianvian cluster.

The Danish results are particularly strong in this paper, owing to the higher number of intact remains recovered. Therefore a very detailed narrative can be constructed of Danish prehistory. The Mesolithic cultures show very close continuity with the material culture record - an almost totally homogeneous and self-contained population for 5,000 years, from the Kongemose, to the Maglemose and finally the Ertebølle. Dietary and mobility isotope data supports the previous findings that early Mesolithic people ate more terrestrial resources, which shifted as the water level rose to a high marine food diet. Mobility was very limited.

The Neolithic Funnelbeaker Culture, which arrived in Denmark around 5,900 BP, showed an almost total population replacement. Nuclear families, eating mostly terrestrial foods, now took over the land. These Neolithic people were more mobile and some ate a wider diet than the previous Mesolithic people. Nobody knows what happened to the previous Ertebølle people…

Finally the incoming Steppe results showed a number of interesting findings:

• The Neolithic had roughly 50 generations before the first Corded-Ware Culture (CWC) Steppe peoples arrived between 4,600 - 4,300 BP. Y-chromosome R1a dominated.

• Around 3,800 BP the populations then clusters with central and western Europeans dominated by males with distinct sub lineages of R1b-L51, including Danish individuals from Borreby and Madesø with distinct cranial features.

• Finally, post 3,800 BP saw the domination of the I1 Y-haplogroup. This population formed the basis for Iron Age and Viking Scandinavians as well as other Germanics such as Anglo-Saxons and Goths. As the authors diplomatically state:

“The rapid expansion of this haplogroup and associated genome-wide ancestry in the early Nordic Bronze Age indicates a considerable reproductive advantage of individuals associated with this cluster over the preceding groups across large parts of Scandinavia.”

Pollen records associated with the Danish results show a pattern of forest clearance and regrowth during the Neolithic period, followed by conversion to forested pasture land once the CWC populations become dominant, reflecting the shift from agricultural dominance to pastoralism.

Steppe Invasions

Previous work had indicated that the CWC may have its origins in the Globular Amphora Culture (GAC), but this has been disputed. The results from this paper demonstrate that the interaction zone and cross-cultural influences between the Yamnaya and GAC were also genetic, and all subsequent markers for steppe ancestry in Western Europe carry the legacy of the Neolithic GAC people as well. This is an incredibly important finding for the work of tracking down the origins and formation of the CWC.

As per previous results - the highest WHG ancestry is in the Baltics, Russia, Belarus and Poland, EHG ancestry in Mongolia, Finland, Estonia and Central Asia and Western Steppe Ancestry highest in Iceland, Ireland, Norway and Sweden.

Britain was broken down extensively by region:

• Highest Steppe ancestry in Outer Hebrides and Ireland

• Highest Neolithic farmer ancestry in southern and eastern England and lower in Scotland, Wales, and Cornwall

• Immigrating Anglo-Saxons had less Neolithic farmer ancestry than the Iron-Age population of southwest Briton

• Higher levels of WHG-related ancestry in central and Northern England

• Taken together, these results show Cornwall and Wales as genetically differentiated regions

Hunter-gatherer resilience east of the Urals

Far less work has been done on the eastern zone hunter-gatherers, but this paper uses new genomic data from 38 individuals - 28 of which date to pottery-associated hunter-gatherer contexts between 8,300-5,000 BP. The “Neolithic Steppe” regions spans the Siberian Forest Steppe zones of the Irtysh, Ishim, Ob, and Yenisei River basins to the Lake Baikal area.

The modelling results showed the following:

• early West Siberian hunter-gatherer ancestry dominated in the western Forest Steppe

• Northeast Asian hunter-gatherer ancestry was highest at Lake Baikal.

• Paleosiberian ancestry in a gradient of decreasing proportions from northern Lake Baikal westwards across the Forest Steppe

Around 3,700 BP waves of migrations from the steppe appear, which occur as pulses and wane. But they show two distinct phases:

• Earlier Yamnaya / Later Sintashta/Adronovo admixed with GAC

• A separate non GAC admixed pulse - Afanasievo/Okunevo

This may have significant implications when considering the spread of Indo-European languages and how Tocharian fits into the historical picture.

Dietary & Immunological Implications for today

The huge data set allowed the researchers to pinpoint 21 genome-wide selection peaks over the last 12,000 years of European prehistory:

• Lactase persistence emerged around 7,000 years ago, prior to the Yamnaya expansions

• Selection in the FAD gene cluster, which is involved in metabolising fatty acids, appeared in the Anatolian farming population. This is strongly associated with a switch from a meat heavy to plant heavy diet

• Various selections for lipid and sugar metabolic alleles, some of which are associated with modern diseases such as diabetes

• Selection for an agricultural diet increased the prevalence of autoimmune diseases, still common in Western Europe

• Alleles on chromosome 17 which cause neurodegenerative diseases such as Alzheimers were prominent in Anatolian farming populations and possibly in the Yamnaya Steppe populations

• Strong selection for lighter skin pigmentation throughout the population transitions

• Yamnaya and Eastern hunter-gatherers showed strong selection for taller stature, a trait which has been differentially passed down into later European populations

• Loci associated with mood-related disorders, like increased anxiety, guilty feelings, and irritability are over represented in Anatolian farmer ancestry

Conclusions

Obviously this is a major paper with many important implications for the study of European prehistory, the agricultural transition, the emergence of the steppe migrations, the origins of the Indo-European languages, modern metabolic pathologies and many more. I haven’t been able to do justice to every result in the paper, especially those which are ambiguous or uncertain. Hopefully this will make reading the paper easier, or at least keep you up to speed with developments in the fast moving world of ancient population genetics.