Category Archives: Palaeogenetics

Second Pandemic Plague Genomes of the 18th Century

Guellil, M. et al. A genomic and historical synthesis of plague in 18th century Eurasia. Proc. Natl. Acad. Sci. U. S. A. (2020) doi:10.1073/pnas.2009677117

Abstract:

Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestisg enomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia,18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.

Second Pandemic Plague Genomes from Poland and Russia

Morozova, I. et al. New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe. Philos. Trans. R. Soc. B 375:20190569 (2020) doi:10.1098/rstb.2019.0569

Abstract:

Yersinia pestis, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of Y. pestis have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled Y. pestis genomes from Eastern Europe(Poland and Southern Russia), dating from the fifteenth to eighteenth century AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern Y. pestis strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial Y. pestis genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning Y. pestis transmission and its evolutionary history in Eastern Europe.

Second Pandemic Plague Genomes From Riga

Susat, J. et al. Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic. Scientific Reports 10:14628 (2020), doi:10.1038/s41598-020-71530-9

Abstract:

Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post‑Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the pla gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the pla gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post‑Black Death strains, but not in the Black Death strains. The pla gene is an important virulence factor for the infection of and transmission in humans. thus, the spread of pla‑depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.

Tropical Diseases in late medieval Northern Europe


K. Giffin/A. K. Lankapalli/S. Sabin u. a., A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe. Scientific Reports 10, 1, 2020, e36666.
doi: 10.1038/s41598-020-66012-x

 

The “application of a non-targeted molecular screening tool for the parallel detection of pathogens in historical plague victims from post-medieval Lithuania” enabled a Jena based research team to show ” the presence of more than one active disease in one individual. In addition to Yersinia pestis, we detected and genomically characterized a septic infection of Treponema pallidum pertenue, a subtype of the treponemal disease family recognised as the cause of the tropical disease yaws. Our finding in northern Europe of a disease that is currently restricted to equatorial regions is interpreted within an historical framework of intercontinental trade and potential disease movements. Through this we offer an alternative hypothesis for the history and evolution of the treponemal diseases, and posit that yaws be considered an important contributor to the sudden epidemic of late 15th century Europe that is widely ascribed to syphilis. “

For a German media report see:

 

Rainer Schreg

archaeologist professor in medieval and postmedieval archaeology at Bamberg university

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Bronze Age plague from Lake Baikal

Along with the publication of 19 ancient human genomes from Paleolithic to Bronze Age Lake Baikal, Yu et al. published two Y. pestis genomes. Remarkably, the two individuals carrying plague show no Yamnaya-related ancestry, in contrast to all previously identified individuals infected with this LNBA plague branch. Another suprising result is that the closest Y. pestis strain in the phylogeny published so far was found in Estonia (Kunila2).

Yu, H. et al. Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia. Cell [in press] (2020) doi:10.1016/j.cell.2020.04.037

Summary:

Modern humans have inhabited the Lake Baikal region since the Upper Paleolithic, though the precise history of its peoples over this long time span is still largely unknown. Here, we report genome-wide data from 19 Upper Paleolithic to Early Bronze Age individuals from this Siberian region. An Upper Paleolithic genome shows a direct link with the First Americans by sharing the admixed ancestry that gave rise to all non-Arctic Native Americans. We also demonstrate the formation of Early Neolithic and Bronze Age Baikal populations as the result of prolonged admixture throughout the eighth to sixth millennium BP. Moreover, we detect genetic interactions with western Eurasian steppe populations and reconstruct Yersinia pestis genomes from two Early Bronze Age individuals without western Eurasian ancestry. Overall, our study demonstrates the most deeply divergent connection between Upper Paleolithic Siberians and the First Americans and reveals human and pathogen mobility across Eurasia during the Bronze Age.

 

The Microbiology of early Globalisation

Blog Entry based on an updated extract from my book “Jenseits von Rom und Karl dem Großen” (Vienna 2018):

preiserkapeller

Byzantinist/medievalist at the Austrian Academy of Sciences with a tendency to experiment with concepts and methodologies from global/environmental history, complexity studies, network analysis.

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CfP EAA Barcelona 2018: Re‐thinking medieval and early modern pestilences from a biosocial perspective: advanced methods and renewed concepts in archaeological sciences

EAA Barcelona 2018 – 5‐8 September 2018
Call for Papers and Posters
Deadline: 15 February 2018
Re‐thinking medieval and early modern pestilences from a biosocial perspective: advanced methods and renewed concepts in archaeological sciences

While contagious diseases have affected the human species since its origins, great medieval epidemics (e.g. plague, leprosy, tuberculosis) have sparked particular interest for decades. In recent years, archaeology has played an increasing role in the scientific study of medieval pestilences, notably by providing reliable data on both the paleobiology of epidemic victims and their burial treatment. Despite the various breakthroughs reached by interdisciplinary research, the study of past epidemics still needs to get improved, particularly through an integrated analysis of biological and social dimensions of these diseases, which are closely interrelated. We invite contributions regarding both recent methodological advances in the retrospective diagnosis of infectious diseases and the output of archaeological sciences on social and cultural factors acting in human populations’ adaptability to these diseases.

The session shall address various questions, among which:
– What are the new lines of research and future perspectives in paleopathological and palaeomicrobiological study of these diseases?
– What information paleobiological data derived from skeletal assemblages can provide on the epidemiological characteristics of the diseases?
– What was the endemicity of diseases in various places, how did they evolve over time, and how did various diseases competed each other?
– How funerary archaeology and textual sources contributes to reappraise the history of these diseases (e.g. attitudes towards the victims in terms of their integration and/or exclusion, depending on the time period and cultural framework)?
– Which methodological implementation would be desirable in the future to allow retrospective diagnosis of still poorly-known diseases (e.g. ergotism)?

Keywords: Archaeology, Paleomicrobiology, Paleopathology, Medieval, Epidemics

Session details:
– Session theme: Theories and methods in archaeological sciences
– Session ID: #413
– Session type: Session, made up of a combination of papers, max. 15 minutes each
Session organizers:
– Dr. Dominique Castex, CNRS, UMR 5199 – PACEA, Université de Bordeaux, Pessac, France, dominique.castex@u-bordeaux.fr
– Dr. Mark Guillon, Inrap, UMR 5199 – PACEA, Université de Bordeaux, Pessac, France, mark.guillon@inrap.fr
– Maria Spyrou, Max Planck Institute for the Science of Human History, Jena, Germany, spyrou@shh.mpg.de
– Marcel Keller, Max Planck Institute for the Science of Human History, Jena, Germany, keller@shh.mpg.de
– Dr. Sacha Kacki, Department of Archaeology, Durham University, United Kingdom, sacha.s.kacki@durham.ac.uk

Abstract submission deadline:
15 February 2018

If you are interested to submit a Paper or Poster proposal, please use the conference website at
https://www.e‐a‐a.org/EAA2018/
Further information, including registration details, general and practical information, etc. can be found on the conference website

EAA Vilnius 2016: Session report on “Plague in diachronic and interdisciplinary perspective”

The following session report by Doris Gutsmiedl-Schümann (Freie Universität Berlin, Germany), Sacha Kacki (Université de Bordeaux, France), Marcel Keller (MPI-SHH Jena, Germany) and Christina Lee (University of Nottingham, UK) will be published in The European Archaeologist. With kind permission of the EAA.

Edit 17-02-07: filmed talks are now linked under the respective name.

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Plague, an infectious disease caused by the bacterium Yersinia pestis, occurred in at least three major historical pandemics: the Justinianic Plague (6th to 8th century), the Black Death (1348-1352, with further epidemic outbreaks until the 18th century), and the Modern or Hong Kong Plague (19th to 20th century). However, it appears that the disease may be much older: DNA from Bronze Age human skeleton has recently shown that plague first emerged at least as early as 3000 BC. As any disease, plague has both a biological as well as a social dimension. Different disciplines can therefore explicate different aspects of plague which can lead to a better understanding of the disease and its medical and social implications.

The session was held on 2nd September 2016 as part of the 22nd Annual Meeting of the EAA with the aim of bringing together researchers from different disciplines who work on plague. It addressed a series of research questions, such as:

  • Which disciplines can contribute to the research on plague?
  • What are their methodological possibilities and the limitations of their methodologies?
  • How can different disciplines work together in order to gain a more realistic and detailed picture of plague in different periods and regions?
  • How did different societies react to plague? In which way may we prove or disprove evidence for such reactions – and which disciplines may contribute to the debate?
  • What where the common aspects, and what the differences of the various plague outbreaks? Are there any epidemiological characteristics that are essential and/or unique to plague?
  • What are possible implications of the pandemic spread and endemic occurrence of plague through the ages for the interpretation of historical and cultural phenomena?

Continue reading EAA Vilnius 2016: Session report on “Plague in diachronic and interdisciplinary perspective”

Introduction – Marcel Keller

I am a PhD student in the department Archaeogenetics of the Max Planck Institute for the Science of Human History in Jena, Germany. My academic background is Biology (B.Sc./M.Sc.) with specialization in Anthropology and Human Biology. The main project of my PhD is the reconstruction of genomes of Yersinia pestis of both the first (Justinianic Plague) and second pandemic (following the Black Death) in Europe. Additional ancient genomes of Y. pestis are crucial for phylogenetic analyses and allow a more detailed picture of the spatiotemporal distribution of plague.

Lepra in the Middle Ages

A new genetic study dealing with Lepra:
V. J. Schuenemann, P. Singh, T. A. Mendum, B. Krause-Kyora, G. Jäger et al., Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae. Science (online 13.6.2013)

There have been several media reports in Germany. E.g. FAZ (19.6.2013)

Rainer Schreg

archaeologist

professor in medieval and postmedieval archaeology at Bamberg university

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y.p. genomes

Just a notice of two posts at Contagions, dealing with recent papers on y.p. genomes:

and at Bones don’t lie:

Rainer Schreg

archaeologist

professor in medieval and postmedieval archaeology at Bamberg university

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Molecular Traces of the Black Death

Over the last decade a substantial amount of molecular evidence confirming the etiology of the plague over virtually the entire medieval period has been produced. In this rapidly evolving field, evidence for the Black Death of the 14th century has been produced by each new method in turn.

Given the conditions of remains sampled to date, the methods fall into two main categories: genomics and immunology. There are pros and cons to each. Genomics has well-recognized specificity and the ability to compare with living and ancient strains, but non-nucleic acid methods are both specific and far more sensitive. Non-nucleic acid methods (using immunology) will give a better indication of the true incidence within a population, especially important when testing moves beyond mass graves. Immunologic methods have been the primary means of diagnosing clinical infectious disease for at least 30 years. The Rapid Diagnostic Test (RDT) now used to diagnose ancient and modern plague uses technology that has existed for over 25 years with a good track record. The downside of immunology is that it doesn’t give strain specific information. On the other hand, detection of degraded DNA much less getting good enough sequence for strain matching is difficult and inefficient.

This map charts all of the medieval plague molecular data that I have seen (view Plague Map in a larger map). The red balloons mark 6th-9th century, Plague of Justinian, sites. All three early medieval sites are beyond the Alps proving that the plague of Justinian penetrated well beyond the Mediterranean basin.  The yellow balloons represent 14th century data, with the starred balloon specifically dated to the first wave of the Black Death pandemic. The blue balloons represent post-14 century data (14th-17th century). Click the balloons for references.

Even a cursory look at the map makes it apparent that both pandemics reached beyond the Alps into the European plain. Further, the distribution represents the areas of activity of 3-4 research groups rather than as an indication of plague incidence across Europe. Every region so far examined and published has found some evidence of plague. There is both DNA and immunological evidence for the 14th century. Unfortunately, DNA data has been produced by three different groups who have not yet produced a consensus sequence or analyzed their differences. Despite the differences between their sequences, there is plenty of homology between their data and modern reference sequences to ensure that they all identified Yersinia pestis. Their differences are most likely to be primarily related to interpretations of degradative changes in the ancient DNA, though it is possible that more than one strain was active in 14th century Europe.

The map also makes it apparent that we only have molecular evidence from a very small sliver of the territory covered by the medieval pandemics. There are too few sites so far to make any predictions about the routes the plague traveled based on molecular evidence. It never travels from point A to point B as the crow flies! Plague spreads more like a spiderweb than a wave. So, long distance transmission may well exist before lateral spread fills in the countryside. It is absolutely necessary to take in consideration medieval trade and communication routes.

This is an exciting time to be working on the plague. So far, only the tip of the iceberg has been exposed. To date, the molecular evidence has been the most useful for confirming the etiology of the plague of Justinian, the Black Death pandemic, and plague’s endurance in western Europe. We have the technology now to map the geographic extent of Yersinia pestis for the first and second pandemic. It will take at least a generation of work from archaeologists, geneticists, and paleomicrobiologists to gather enough sites and resolve the fine-detail sequencing issues to begin to do strain mapping.