Breakdown: Ancient European Genetics Papers of 2024 - Part One

Populations turnovers, ancient phenotypes, multiple sclerosis and Danish prehistory

It’s only February and already there are more genetics papers than I can comfortably review and digest. In fact there are so many I need to split this up and write multiple articles. So for Part One I have FOUR papers for you, all focused around the transition from the Mesolithic to the Bronze Age, the time period that has really become the focal point of modern archaeogenetics.

These four papers are all connected - they come out of the same research projects, they are all written by the same group of researchers and they were all published on the same day, January 10th 2024. What we see here is the creation of a dataset so rich, that they had to split their analyses into four separate papers, with hundreds of pages of supplementary data and over ten spreadsheets worth of genetic and isotope data available to the public. Let’s jump in -

Paper One: Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations

I recall seeing this paper as a preprint a few years, which has now been published in Nature. I believe that the lead author, William Barrie, has been working on this topic for his PhD (he’s on Twitter if you want to follow his work). The subject is fascinating - tracing the cause for why northern Europeans have such an elevated risk for multiple sclerosis (MS), a neurodegenerative autoimmune disease. To do this the researchers took apart MS genetics at the population level. Firstly they assessed what genetic variants are involved in MS:

Genome-wide association studies (GWAS) have identified 233 commonly occurring genetic variants that are associated with MS; 32 variants are located in the human leukocyte antigen (HLA) region and 201 are located outside the HLA region . The strongest MS associations are found in the HLA region, with the most prominent of these, HLA-DRB1*15:01, conferring an approximately threefold increase in the risk of MS in individuals carrying at least one copy of this allele.

Since MS is not just a genetic disease, but rather a combination of environmental and genetic factors, the whole story cannot be explained by ancestry alone. But the target of study was identified, the HLA region, which is a cluster of genes on chromosome 6 involved in immunity. Next they managed to compile an impressive database of over 1,700 human genomes spanning the 10,000 years from the Mesolithic to the present day, covering virtually the whole time period. These included modern individuals from the UK Biobank. Then they looked for genetic variation within this huge dataset which corresponded to an increased risk of MS. What makes this possible is the work that's been done since 2015 to understand how European prehistory was structured at the population level. We now know that post ice-age Mesolithic ‘Western Hunter Gatherers’ were largely replaced and occasionally assimilated by incoming Neolithic farmers, who were themselves routed and adopted by the later steppe invasions.

Looking at the ‘steppe’ population through time, the researchers identified that this ancestral group carried significantly more genetic markers for MS than any other group, producing a higher risk of the disease in both themselves and their descendants. The final question then is why? Why did steppe populations carry these risk factors? The answer lies in their exposure to diseases, both from animals, other humans and novel pathogens. The steppe was the highway of Eurasia, and as these hunter-gatherers took up pastoralism and eventually horses, they promoted a range of genetic variations which could help them cope with the disease load. Unfortunately, the the absence of these pressures today, what was a help became a hindrance, and the autoimmune attacks of MS became a part of northern European life.

Our interpretation of this history is that co-evolution between a range of pathogens and their human hosts may have resulted in massive and divergent genetic ancestry-specific selection on immune response genes according to lifestyle and environment followed by recombinant-favouring selection after these populations merged… Together, these findings indicate that population dispersals, changing lifestyles and increased population density may have resulted in high and sustained transmission of both new and old pathogens, driving selection of variants in immune response genes, which are now associated with autoimmune diseases.

Paper Two: The selection landscape and genetic legacy of ancient Eurasians

The second paper is another advance on previous work that uses these ancient European genomes to compare health and phenotype distributions to modern populations. Again, to reiterate, these studies are only possible because of the work done to identify the separate groups which form the genetic basis for modern European peoples.

This time we have over 1,600 ancient genomes running from Lake Baikal to Ireland, Scandinavia to the Middle East, over a time period from 10,000 years ago to around 1000 AD. They compared these with over 400,000 UK Biobank samples looking at 35 different complex traits. It’s worth reading the paper yourself if just for the visual maps and diagrams, in particular a very fine detailed map of Britain and Ireland showing how much ancestral contribution comes from either: Eastern Hunter-Gatherers (EHGs), Caucasus Hunter-Gatherers (CHGs), Western Hunter-Gatherers (WHGs), Steppe groups and Neolithic farmers.

The team designed some clever modelling techniques to work backwards from the modern samples to test whether certain traits had been actively selected for or against over time, or whether trait differences were a product of different ancestral proportions. They found 21 selection peaks that mapped onto the different ancestries, including:

• Lactase persistence (ability to drink milk as an adult)

• Fatty acid metabolism

• Sugar metabolism

• Immunity

• Digestion

• Skin pigmentation

• Cardiovascular disease

To give one example - the team found many examples of systemic disease risk factors associated with the oldest Mesolithic populations in Europe, the hunter gatherer peoples. These included expressions of gene variants involved in salt and fat metabolism, cardiovascular disease, diabetes and cholesterol disorders. To quote from the paper:

These may represent selection episodes that preceded the admixture events described above and led to differentiation between ancient hunter-gatherer groups in the late Pleistocene and early Holocene. One of these overlaps with the SLC24A3 gene, which is a salt-sensitivity gene significantly expressed in obese individuals. Another spans ROPN1 and KALRN, two genes involved in vascular disorders. A further region contains SLC35F3, which codes for a thiamine transport and has been associated with hypertension in a Han Chinese cohort. Finally, there is a candidate region containing several genes (CH25H and FAS) associated with obesity and lipid metabolism and another peak with several genes (ASXL2, RAB10, HADHA and GPR113) involved in glucose homoeostasis and fatty acid metabolism. These loci predominantly reflect ancient patterns of extreme differentiation between Eastern and Western Eurasian genomes and may be candidates for selection after the separation of the Pleistocene populations that occupied different environments across the continent (roughly 45,000 years ago)

If I had to infer what this meant, I’d suggest it likely reflects Mesolithic adaptations to a diet rich in seafood, omega-3 fatty acids and relatively low levels of carbohydrate. The reason these are implicated as risk factors is that the European diet from the Neolithic onwards is based on high amounts of cereal grains, with increasing amounts of dairy and ruminant fat as time goes on. Hunter-gatherers and horticulturalists the world over suffer tremendously on modern diets, as evidenced by the soaring rates of diabetes and obesity in places like Polynesia.

Finally the diagram below shows the ancestral risk scores for the 35 complex traits in modern populations. For most of these we see ancestral gradations across Europe, for instance people being taller where steppe ancestry is more prevalent.

This is a very detailed paper, and I have barely scratched the surface here. The supplementary data is over 200 pages long, containing a wealth of information about all the genetics and risk factors broken down by ancestry. As I’ve said before in previous articles, we’re entering into an age where genetics and archaeology can determine the biological course of human life like never before - soon we will get lineages of families traced across time, with their health, diet and phenotypes broken down and how their kinship networks were structured.

Paper Three: Population genomics of post-glacial western Eurasia

This paper was also released a while back as a pre-print, another one by Allentoft and his team. His 2015 paper on the genetics of the steppe and the bronze age is now a landmark study, kickstarting this era of population genetics and sweeping away decades of theoretical work. For more background into the fine-grained detail of European population genetics you can read articles I’ve written here and here, which help explain how certain groups were formed and transformed.

This paper develops themes identified in earlier papers, giving all the relevant citations for the now familiar story about how agriculture moved into Europe and then the rise and spread of the steppe peoples which came later. Through this we can now see where the gaps are in our knowledge, and they include:

• Mesolithic demographics older than around 6,000 BC

• How and why European hunter-gatherers were genetically split around eastern Europe, and how the eastern group interacted with incoming farmers

• The population structure of the pottery-using hunter-gatherers in Siberia/Central Asia

• The origins of the steppe ancestry sources (northern steppe and southern Caucasus)

• The reason why steppe ancestry haplogroups change as they enter into Europe (R1b vs R1a)

Using the same dataset as previously described in the other papers, the researchers first began by constructing population models through time and space, which produced some new results for our story:

• A new Palaeolithic skeleton from Kotias Klde Cave in Georgia (ca 24,000yo) was sequenced and found to be the new best source for Western Hunter Gatherer ancestry, with Eastern Hunter Gatherers closest to a skeleton from Mal’ta (Lake Baikal) from 22,000 years ago.

• Denmark will be dealt with in another paper, but southern Swedish hunter-gatherers contained a huge amount of southeastern European ancestry, previously described as ‘Ukrainian’ but now as ‘Romanian’.

• Scandinavian hunter-gatherers can be modelled from three waves of immigration, from southern Europe, from southeastern Europe and then from Russia down the Norwegian coastline. This seems in line with what was already known from genetics and inferred from stone tool analysis.

• Iberian populations also received a similar wave of southeastern migration, indicating that an exodus from a glacial refugia between Ukraine and Romania took place prior to the arrival of Neolithic farmers.

• Two new genomes from the Pontic-Caspian steppe (ca 5,300 BC) were found to be a mixture of this Ukranian/SE population along with an unexpected amount of Caucasus/Iranian derived ancestry, suggesting that such mixing on the steppe was occurring long before ‘steppe ancestry’ or Yamnaya populations developed.

• The great east-west divide, from the Baltic to the Black Sea was confirmed by the study and solidified a truly incredible picture - on the western side of the line, most hunter-gatherers were replaced by farmers, with a few exceptions and some moments of resurgence - but on the eastern side there was no genetic change at all until the rise of the steppe peoples.

• Yamnaya/Steppe ancestry can be best modelled as 65% Middle Don genomes and 35% hunter gatherers from the Caucasus. This is a huge result, as the exact origins of the steppe ancestry has been debated for a while now. Here they present several genomes from the site of Golubaya Krinitsa, where the exact ancestry ratios of CHG/EHG are correct for all later derived steppe peoples.

• Movement from the steppe into Europe now looks incredibly complicated. The picture of horse mounted raiders sweeping into agricultural communities seems wholly wrong now - for a start, all steppe ancestry input came from the Corded Ware Culture which in turn derived its steppe ancestry from groups which were themselves a mixture of steppe and farming peoples (Globular Amphora Culture).

• The exact reason why the paternal genetics look different from Yamnaya to Corded Ware is still unknown, as they say “currently published Yamnaya-associated genomes do not represent the most direct source for the steppe ancestry component in CWC”

These are just highlights and for the sake of brevity I’ve skipped the section on eastward hunter-gatherers between the Urals and Lake Baikal, but for those interested in more eastern Eurasian genetics the paper has a clear marked section on the topic.

They also give an explanation for why they think the east-west divide was so strong, but we are at early days with this research and the invasion of Ukraine has set back excavations and research in this crucial area of study, so we may have to wait a while to fully elucidate the reasons why this genetic divide existed:

In eastern Europe, the expansion of Neolithic farming was halted for around 3,000 years, and this delay could be linked to environmental factors, with regions east of the division having more continental climates and harsher winters, possibly less suited for Middle Eastern agricultural practices⁶⁹. Here, highly developed HG societies persisted with stable, complex and sometimes fortified settlements, long-distance exchange and large cemeteries^70,71. A diet including freshwater fish is clear both from our isotopic data (Supplementary Data 2) and from analyses of lipids in pottery⁷¹. In the northern forested regions of this boundary zone, HG societies persisted until the emergence of the CWC around 5,000 cal. BP, whereas in the southern and eastern steppe regions, hunting and gathering was eventually complemented with some animal husbandry (cattle and sheep), and possibly horse herding in central Asia⁷². Some of these groups, such as Khvalynsk at the Volga, saw the emergence of male sodalities involved in wide-ranging trade connections of copper objects from east central Europe and the Caucasus²⁹. Settlements were confined mainly to the flat flood plains and river valleys, whereas the steppe belt remained largely unexploited.

Overall this is another very dense paper, with huge implications for future research. It potentially closes the door on one very big question, where the steppe ancestry originated from, as well as fleshing out many major demographic transitions.

Paper Four: 100 ancient genomes show repeated population turnovers in Neolithic Denmark

Finally we get to the last paper. This is essentially a continuation of the previous paper, but focused on Denmark specifically. The number of human remains and quality of archaeological evidence from the Mesolithic onwards makes Denmark the perfect place to study postglacial demography. In this paper then we get 100 genomes to see how Denmark evolved from the Ice Age to the Bronze Age.

Denmark’s archaeological chronology is extremely well documented, running through three stages of Mesolithic life: (Maglemose, Kongemose and Ertebolle), then the Neolithic Funnel Beaker Culture and the Single Grave Culture to the Bronze Age. Taking 100 genomes from across this timespan, Allentoft and his team produced the following insights:

• The Danish Mesolithic was insular and homogenous, deriving from the same WHG sources as the rest of western Europe, with some very weak eastern flow at the beginning of their settlement.

• Danish WHGs were so tightly knit that they don’t overlap with Swedish WHGs, despite their proximity. The use of pottery and particular tool types which came from elsewhere demonstrate that cultural diffusion was the process of information sharing.

• Their diet became ever more seafood oriented as the sea levels rose, switching their protein sources from land animals to shellfish, marine fish and seaweed.

• The Neolithic saw a complete and total turnover of this group. The Danish WHGs did not survive. Towards their final years, there is a small amount of gene flow from them to the Funnel Beaker Neolithic farmers, and a few individuals had adapted to the Neolithic diet and lifeways despite being of WHG origin (Dragsholm Man, Syltholm birch tar genome). How they disappeared is unknown.

• Around 2,800 BC the Corded Ware Culture arrived, known locally as the Single grave Culture. This again transformed Denmark demographically, turning over the population towards the newcomers, rich in steppe ancestry. Although the diet did not change much, the average height increased.

• Then we reach the Late Neolithic Dagger phase, which saw three distinct moments:

  • LNBA phase I: an early stage between around 2,600 and 2,300 BC, in which Scandinavians cluster with early Corded Ware individuals - males with an R1a Y chromosomal haplotype.

  • LNBA phase II: an intermediate stage largely coinciding with the Dagger epoch (around 2,300–1,700 BC) - dominated by males with distinct sub-lineages of R1b-L51

  • LNBA phase III: a final stage from around 2,000  BC - dominated by males with I1 Y-haplogroups. Y chromosome haplogroup I1 is one of the main haplogroups in modern Scandinavians

Using genomes from LNBA phase III (Scandinavia_4000BP_3000BP) in supervised ancestry modelling, we find that they form the predominant ancestry source for later Iron and Viking Age Scandinavians and other ancient European groups with a documented Scandinavian or Germanic association (for example, Anglo-Saxons and Goths)

The authors provide this incredible graphic, which neatly slots together an incredible amount of information, from environmental impact to eye colour, diet to paternal lineage. The kind of information former archaeologists could only dream of.

I’ll leave this long and rather dry summary article with a quote from Allentoft:

It remains a mystery why the Neolithic farming expansion came to a 1,000-year standstill before entering Southern Scandinavia. It may be that it was complicated by a high Mesolithic hunter-gatherer population density owing to a very productive marine and coastal environment^20,65. Further, the Danish Ertebølle population may have been acquainted with armed conflict^11,66 enabling territorial defence against intruders. Alternatively, it has been argued that changing climatic conditions around 6,000 cal. BP became a driver since it enhanced the potential for farming further north⁶⁷, but other studies have not confirmed this⁶⁸. The second population turnover in the late Neolithic resulted in a short period of three competing cultural complexes in Denmark, namely the FBC, the PWC and the SGC. The latter introduced the steppe-related ancestry which has prevailed to this day. There is archaeological evidence that this was a violent time, both in Denmark⁶⁹ and elsewhere^70,71. Additionally, ancient DNA evidence has demonstrated that plague was widespread during this period^72,73. In tandem with other indicators of population declines⁷⁴, and widespread reforestation after 5,000 cal. BP⁷⁵, it suggests that the local populations of Central and Northern Europe may have been severely impacted prior to the arrival of newcomers with Steppe-related ancestry. This could explain the rapid population turnover and limited admixture with locals we observe.