CRC 1266 - Scales of Transformation

Research activities 2016-2019

Infections are thought to have accompanied Homo sapiens throughout evolution, and many epidemics may have influenced important prehistoric transformation processes. Project F4 aims to evaluate whether pathogens co-occurred with major demographic and/or environmental crises in the past.

Large-scale pathogen screening

Although ancient DNA (aDNA) research has in general made huge progress over the last decade, it is still challenging to diagnose infectious diseases in human skeletons by genetic methods, mainly due to poor preservation. Another obstacle is that many infections do not leave specific lesions on the bone, making it difficult to link them to the pathogens that cause them. In the absence of such external guiding factors, a targeted sampling is not possible and the detection of a pathogen is virtually a chance finding. To increase the odds of success, the investigation of hundreds or thousands of human remains is required - and a tiny bit of luck. The large-scale pathogen screening is the main focus of the subproject F4 in the first phase of the CRC 1266. The aDNA extracted from the samples is subjected to high-throughput sequencing and the generated data is analysed using bioinformatic methods. In this way, it is possible to identify genetic leftovers of both bacteria and viruses and to trace their evolutionary history.

Up to now, we have collected human material (teeth, petrous bones) from about 1000 skeletons excavated from 30 sites across Germany as well as northern and eastern Europe (e.g. Czech Republic, Moldova, Romania). The specimens date to different periods ranging from the Early Neolithic to the Late Bronze Age (5500 - 1500 BCE) and thus cover a large part of the diachronic focus of CRC1266. Further sampling is still ongoing.

In 2 out of 53 Neolithic skeletons from central Germany, we recovered the full genomes of the hepatitis B virus (HBV) in individuals associated with the Linear Pottery and the Funnel Beaker Culture, respectively. The Neolithic HBV strains appear to represent distinct lineages that no longer exist today and thus likely went extinct. One of the infected individuals dates to 7000 years ago and is the hitherto oldest known HBV carrier (Krause-Kyora et al., 2018a). This study was performed in collaboration with subproject D2 and the Max Planck Institute for the Science of Human History in Jena.

So far, we have investigated about 700 Neolithic and Bronze Age remains for infectious microbial agents. Despite this tremendous effort, we have found - with the exception of Helicobacter pylori (Maixner et al. 2016) and HBV - no evidence of further infectious agents. This result challenges the previous research hypothesis that socio-economic transformations during the Neolithic could be triggered or influenced by epidemics. However, we are aware of the limitations given by the preservation of the bioarchaeological records and the absence of evidence may be due to the fact that only blood-borne DNA-containing pathogens can be detected in skeletal material and that pathogens infecting other tissues or organs (e.g. intestines) or RNA viruses will be missed. Thus, the actual infection rate in the Neolithic/Bronze Age might be underestimated. New results from our ongoing screening or the literature may change the picture we have drawn here at any time.

With respect to potential triggers and components of change in Neolithic Germany (with special focus on the loess zone), we reviewed the occurrence of pathogens together with archaeological and palaeopathological proxies (in cooperation with D2 and Z1). The comparison showed that major transformations in domestic strategies and mortuary practice did take place between 5500 and 2500 BCE, but evidence is missing for drawing a causal link between these changes and the presence of pathogens or indicators of skeletal pathology. In particular, palaeopathological parameters for identifying lesions caused by infectious diseases are often unspecific and reported in an inconsistent manner, hampering diachronic interpretations (Fuchs et al. 2019).

Human immune gene evolution

If pathogens are no longer detectable in old bones, the analysis of human immune genes can provide indirect inferences about infectious diseases in the past. In the course of evolution, humans and pathogens have been involved in long-standing reciprocal evolutionary processes, in which the hosts are constantly forced to adapt to new microbial attack strategies. Consequently, their immune defence and the genes responsible for it are altered in such a way that infections can be fought more effectively. In principle, such genetic adaptations can also be studied in prehistoric individuals.

We have started a small pilot study, which is outside the original scope of this subproject, to test the feasibility of such an approach for the planned second phase of the CRC1266. To this end, we have focused on the human leucocyte antigen (HLA) region that encompasses a number of very important immune genes. First, we have established a method for HLA gene capture and a semi-automatic bioinformatics pipeline to reliably determine the alleles in the old individuals (Krause-Kyora et al. 2018b). Subsequently, we successfully generated HLA data sets from 69 Neolithic skeletons, demonstrating the suitability of the applied methods. The results show significant frequency changes of some alleles over time (Fig. 1.), probably due to pathogen-driven selection. Findings like this are also relevant for medical research as they allow us important insights into the evolutionary history of diseases and their genetic predisposition.

Diagramm Abnahme der Frequenz eines HLA-Allels vom Paläolithikum bis zur Neuzeit
Fig. 1. Decrease in the frequency of an HLA allele from the Paleolithic period to modern times (blue line, red line represents a regression curve). Numbers of individuals investigated at each time point are given in brackets. Frequencies are based on data published previously (Mathieson et al. Nature 528: 499-503, 2015; Lazaridis et al. Nature 513:409-413, 2014; Haak et al. Nature 522: 207–211, 2015; Mathieson et al. Nature 555: 197-203, 2018) and generated in subproject F4.

Kinship, phenotype and palaeopathology

When the human aDNA preservation is good enough and the generated shotgun datasets are of sufficient quality, we use the genetic information also for population genetic investigations and kinship analyses as well as phenotype reconstruction of the individuals. In addition, we aim at correlating the obtained results with palaeopathological lesions on bones (Fig. 2.). This study is performed in close collaboration with subprojects D1 and D2.

Foto eines Schädels eines 3-4-jährigen Kleinkindes, welches im Wartberg-Galeriegrab von Niedertiefenbach begraben wurde
Fig. 2. Skull of a 3-4-year-old infant buried in the Wartberg gallery grave of Niedertiefenbach. The orbital roofs show a severe form of trabecular growth, called cribra orbitalia, which are a symptom of increased erythrocyte production due to anemic conditions. These can be a result of physical stress such as malnutrition, increased blood loss or infections. (photo: S. Jagiolla)

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