Category Archives: Palaeogenetics

Archaeology, Axis I - 14th Century Crisis, Epidemiology, Microbiology, Palaeogenetics

Salmonella enterica subsp. enterica serovar Paratyphi C at Lübeck – an outbreak of enteric paratyphoid fever in 1367?

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Excavation in the 1990s at Lübeck Heilig-Geist spital revealed a mass burial with more than 800 individuals dated to the 14th c.  New research screened aDNA from 92 individuals for the presence of pathogens. The analysis resulted in a detection of Salmonella enterica subsp. enterica serovar Paratyphi C.

These results show once more the complexity of the 14th c crisis, which can not be reduced on the BlackDeath.

  • M. Haller/K. Callan/J. Susat u. a., Mass burial genomics  reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lübeck. iScience 24, 5, 2021, 102419. – doi 10.1016/j.isci.2021.102419

A German press report at

Rainer Schreg

archaeologist professor in medieval and postmedieval archaeology at Bamberg university

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Microbiology, Palaeogenetics, Researchers

Introduction – Gunnar Neumann

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I am a PhD student at the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History in Jena, Germany, soon moving to the MPI for Evolutionary Anthropology in Leipzig.

My research focus are ancient pathogens in western Eurasia and their evolutionary history. Among others, I work on Yersinia pestis from the Late Neolithic/Early Bronze Age until late medieval times. 

 

Gunnar Neumann

PhD student at the Department of Archaeogenetics of the Max Planck Institute for the Science of Human History, Jena

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Axis II - History of Plague, Palaeogenetics, Publications and Resources

More Bronze Age Plague from Lake Baikal

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Kılınç, G. M. et al. Human population dynamics and Yersinia pestis in ancient northeast Asia. Science Advances 7, eabc4587 (2021) doi:10.1126/sciadv.abc4587

Abstract:

We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis. Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.

Comment:

After Yu et al. 2020, this is the second Bronze Age plague genome from Lake Baikal. Since this paper was probably submitted before the publication of Yu et al. 2020, this is not discussed here, and the claim that they report the most northeastern Y. pestis genome does not hold true. Unfortunately, the coverage of their genome is extremely low, so it could not be phylogenetically assessed.

Marcel Keller

Co-Editor of the Black Death Network Postdoc in Palaeogenetics at U. of Tartu

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Axis II - History of Plague, Palaeogenetics, Publications and Resources

Second Pandemic Plague Genomes of the 18th Century

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Guellil, M. et al. A genomic and historical synthesis of plague in 18th century Eurasia. Proc. Natl. Acad. Sci. U. S. A. 117 (45) 28328-28335 (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.

Marcel Keller

Co-Editor of the Black Death Network Postdoc in Palaeogenetics at U. of Tartu

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Archaeology, Axis II - History of Plague, Palaeogenetics, Publications and Resources, Zooarchaeology

Second Pandemic Plague Genomes from Poland and Russia

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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.

Marcel Keller

Co-Editor of the Black Death Network Postdoc in Palaeogenetics at U. of Tartu

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Archaeology, Axis II - History of Plague, Palaeogenetics, Publications and Resources

Second Pandemic Plague Genomes From Riga

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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.

Marcel Keller

Co-Editor of the Black Death Network Postdoc in Palaeogenetics at U. of Tartu

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Axis I - 14th Century Crisis, Axis II - History of Plague, Epidemiology, Palaeogenetics, Publications and Resources

Tropical Diseases in late medieval Northern Europe

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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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Axis II - History of Plague, Palaeogenetics, Publications and Resources

Bronze Age plague from Lake Baikal

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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.

 

Marcel Keller

Co-Editor of the Black Death Network Postdoc in Palaeogenetics at U. of Tartu

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Archaeology, Axis II - History of Plague, Climatology and Climate History, Ecology, History, Palaeogenetics, Publications and Resources

The Microbiology of early Globalisation

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a  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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Archaeology, Axis I - 14th Century Crisis, Axis II - History of Plague, Conferences and Workshops, Ecology, Epidemiology, Geoarchaeology, Palaeogenetics, Physical Anthropology

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

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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

Marcel Keller

Co-Editor of the Black Death Network
Postdoc in Palaeogenetics at U. of Tartu

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Archaeology, Axis I - 14th Century Crisis, Axis II - History of Plague, Conferences and Workshops, Ecology, Epidemiology, History, Microbiology, Palaeogenetics, Physical Anthropology, Zooarchaeology

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

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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” →

Marcel Keller

Co-Editor of the Black Death Network
Postdoc in Palaeogenetics at U. of Tartu

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Microbiology, Palaeogenetics, Researchers

Introduction – Marcel Keller

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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.

Marcel Keller

Co-Editor of the Black Death Network
Postdoc in Palaeogenetics at U. of Tartu

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Axis I - 14th Century Crisis, Palaeogenetics, Publications and Resources

Lepra in the Middle Ages

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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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Axis II - History of Plague, In News and Media, Palaeogenetics

y.p. genomes

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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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