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Human health and migration in prehistory

Periodic Reporting for period 2 - PALEoRIDER (Human health and migration in prehistory)

Reporting period: 2019-10-01 to 2021-03-31

Even before the recent COVID-19 related pandemic, human health and mobility were central topics in today’s media, and of constant significance to government agencies as well as most pertinent to current European affairs, as they directly affect human societies, past present and future. The PALEoRIDER project investigates the role of human mobility, infectious diseases, and their interplay in the formation of Europe. At present, we can only record the current status, but – most crucially – we lack a temporal perspective that allows us to characterize the transformative effects that mobility and communicable diseases had on prehistoric societies. A critical understanding of the mobility and migration in Europe’s prehistory, the evolutionary relationships between human and animal hosts and pathogens, cause and effect of past exposure to pathogens, infectious diseases, and the adaptability to varying (man-made) environments and changing climate is of paramount importance, as it can inform decision-making processes and future directions in human health and sustainability.
With the new technological advances at hand, it is possible to gain insight into how mobility and health have influenced the course of history in Europe and how they have shaped the genetic makeup of Europeans. PALEoRIDER is currently generating and analyzing an exceptionally detailed record of the genetic history of Europe through the last 8,000 years from a unique collection of over 1000 ancient human remains from key regions that experienced massive transformative changes in the past. Building on strong multi-disciplinary contextualization, our high-resolution genomic transect of human genome, pathogen and metagenomic data will allow a precise genetic characterization of past populations, their disease load and immunity status, crucial for the reconstruction of co-evolution with pathogens, modes of dispersal and interaction, and estimates of admixture between past populations. Importantly, the new analyses are focusing also on the details of the processes and dynamics that have shaped the human genome as expanding populations encountered the challenges of becoming expanding ‘civilizations’. These include adjusting to new food sources, new environments and changing climates, massive population growth, and new infectious diseases, which were linked to major shifts in subsistence strategy and revolutions in culture and social structure. To this effect, we are integrating large-scale genomic sequence data from humans and their immune system, as well as their pathogens through time.
The transformative changes in Europe during the 3rd millennium BC provide an ideal test scenario for questions that are related to human mobility, adaptability and susceptibility to infectious diseases in the past. Central and eastern Europe, two of our key regions of interest, fulfil a number of important criteria that make it an ideal place for selection scans through time. These include excellent sample preservation, a contiguous, diachronic record of settlement history accompanied by world-class archaeology, which guarantees full inter-disciplinary contextualization with available metadata from archaeology, anthropology and paleopathology, biochemistry and geology, and paleoclimatology. Importantly, with genomic data from over 500 ancient European individuals with secured contexts (including radiocarbon and often Sr/O data) available, there is no other region in the world that would allow an unbiased assessment of selection at this scale. With high-quality genome-wide data from ancient humans and pathogens, coupled with state-of-the-art contextualization, we are addressing the following objectives in order of significance and feasibility:
1. Understanding population structure and human mobility
2. Pathogen detection and pathogen evolution.
3. Human pathogen co-evolution.
4. Pathogen ecology and epidemiological modeling.
The first 30 months of the project were used to process and generate genomic data from ~1000 individuals from key sites in prehistoric Europe that span the 3rd millennium BCE. As a standard procedure we screened in parallel for the presence of endogenous human and pathogen DNA. Suitable samples were then subjected to targeted genome capture of known informative variants in the human genome and for complete genomes of candidate pathogens.
A critical aspect of ancient DNA data is the ability to produce time transect in various regions of Europe that can attest allele frequency shifts of certain variants through time or presence/absence and evolution of pathogens, resulting in a time-stamped aDNA record of the states before, during and after, which can then be reconciled with the archaeological context and precise radiocarbon dating.
At the mid-point, the PALEoRIDER project is most advanced in objectives 1 and 2 (see above), which constitute the main aims and provide the main essential prerequisites for further exploration as part of objectives 3 and 4 in the second half of the project. Time transect data from spanning from the 4th to the 2nd millennium BCE is now available from a sufficiently large number of regions, which will eventually permit pan-European comparisons. At this stage the regional details of the dynamic shifts seen in the 3rd millennium BCE Europe are the main focus of the project’s attention. We particularly targeted the transitions from the later phases of the Eneolithic or Copper Age to the Bronze Age in various regions spanning from the North Caucasus in the East to southern Iberia in the West. Here, the presence and expansion of genetic ‘steppe ancestry’ primarily associated with pastoralist groups from the Eurasian steppes is a prominent feature of many of our regional studies. However, it is unclear how this process had led to further transformations of the genetic and social structures in central and western parts of Europe, which are not directly linked to the steppe as an eco-geographic zone and pastoralism as main subsistence strategy.
Our results of ancient human genome data from the late 4th millennium BCE indicate an unprecedented level of dynamism already before the main genetic turnover event, which is currently best observed in tell sites from southeastern Europe, as well as high-densities regional transect in central European settlement areas such as Bohemia, Moravia and central Germany. We also find that the arrival and expansion of steppe ancestry across Europe from the East, which was seen as a unified main turnover event of the early 3rd millennium BCE, can be divided into two or more streams with regional differentiation and slightly variable timing, likely linked to varying population densities and socio-economic characteristic of the prehistoric societies involved. In the following centuries of the 3rd and the early 2nd millennium BCE we observe a complex and regionally varying interplay of groups that are both high and low in steppe ancestry, indicating a long process of assimilation and continuous population dynamics.
Intra-site studies involving biological kinship and uniparentally inherited lineages (e.g. Y-haplogroups) reveal striking patterns of patrilocality and patrilineality alongside a strong reduction in Y-diversity, which suggest isolated mating network under seemingly strict social norms. However, this pattern is dissolves again in the early 2nd millennium BCE in line with new burial customs and potentially reformed social organization.
With respect to pathogens as potential driver or parameter that warrants consideration, we can corroborate previous evidence for the presence of a number of pathogens, in particular two early forms of the plague-causing agent of Yersinia pestis during the early Bronze Age alone. The regular detection and presence of other pathogens (e.g. Salmonella enterica) and recent advances in the detection of prehistoric viruses (e.g. Hepatitis B (HBV) add further to the complex entanglement of human-pathogen interaction in parallel/contrast to human agency alone.
The size of the dataset has also grown beyond what was originally anticipated, which in combination with attention to completion of either chronologically gapless or regionally coherent time transects forms an evermore powerful framework for data exploration. The use of DNA capture techniques has proven to be a central factor for the successful retrieval of genome-wide data that allows sufficiently large cohort sizes, which in turn enable meaningful frequency-based estimates of allele shifts over time. The latter has been critical for the establishment of a large dataset of individuals for which genes and regions with immune genetic (e.g. HLA) or other phenotypic relevance have been enriched. The same holds true for the newly established high-resolution capture of the non-recombining parts of the Y chromosome, which analogous to the mitochondrial and X chromosome complements the exploration of uni-parentally inherited markers, that are used to assess the effects of sex bias during migration and admixture processes.
The latter is also very useful in a related aspect, that of intra-site kinship studies, which we have targeted at a number of sites, which provided ideal settings. Here we compare the social and biological kinship structures of Neolithic, Copper Age and Early Bronze Age groups ranging from largely synchronous multiple burials or complete graveyards of several dozens of graves to demographic and kinship patterns in long-term settlements such as hilltop and tell sites.
On the basis of the already established dataset of human genomic and immune genetic data as well as the unexpectedly large number of detected pathogens thus far we are confident to steer the project in the direction of the objectives 3 and 4 during the next phase. Here, we will attempt to align and synchronize the allele frequency patterns over time from human genomic data with the timed occurrence of pathogen across space and time in light of the archaeological and anthropological context.