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      Beyond Plague Pits: Using Genetics to Identify Responses to Plague in Medieval Cambridgeshire

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Ancient DNA from Yersinia pestis has been identified in skeletons at four urban burial grounds in Cambridge, England, and at a nearby rural cemetery. Dating to between ad 1349 and 1561, these represent individuals who died of plague during the second pandemic. Most come from normative individual burials, rather than mass graves. This pattern represents a major advance in archaeological knowledge, shifting focus away from a few exceptional discoveries of mass burials to what was normal practice in most medieval contexts. Detailed consideration of context allows the authors to identify a range of burial responses to the second pandemic within a single town and its hinterland. This permits the creation of a richer and more varied narrative than has previously been possible.

          Abstract

          L'ADN ancien de Yersinia pestis a été identifié parmi les squelettes provenant de quatre cimetières urbains à Cambridge en Angleterre et dans un cimetière de la campagne environnante. Ces sépultures datant d'entre 1349 et 1561 apr. J.-C. contenaient des individus morts de la peste lors de la seconde pandémie de peste en Europe au Moyen Âge. La plupart avaient été enterrés dans des tombes individuelles ordinaires et non dans des fosses communes. Ce résultat marque une avancée majeure en archéologie en mettant l'accent sur les pratiques funéraires courantes au Moyen Âge plutôt que sur quelques découvertes exceptionnelles de fosses communes. Une considération détaillée des contextes des sépultures permet aux auteurs d'identifier les diverses réactions envers la seconde pandémie de peste à Cambridge et aux alentours et de formuler un récit plus fourni qu'auparavant. Translation By Madeleine Hummler

          Abstract

          Vier Friedhöfe in der Stadt Cambridge in England und ein ländlicher Kirchhof in der Umgebung lieferten Nachweise auf Yersinia pestis mittels alter DNA. Die Skelette, die zwischen 1349 und 1561 datieren, gehören zu Individuen, die der zweiten Pest pandemie zum Opfer fielen. Die meisten stammen aus regelhaften Einzelgräbern und nicht aus Massengräbern. Dieses Ergebnis stellt einen wesentlichen Fortschritt für die archäologische Forschung dar, da es den Fokus weg von einigen wenigen außergewöhnlichen Massengräbern verschiebt und den Schwerpunkt auf normale mittelalterliche Grabsitten legt. Die detaillierte Untersuchung des Kontexts der Bestattungen erlaubt es, eine Serie von Reaktionen auf die zweite Pest Pandemie innerhalb einer Stadt und ihrer Umgebung zu identifizieren und ein differenzierteres Bild als zuvor zu schildern. Translation By Madeleine Hummler

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          Improved metagenomic analysis with Kraken 2

          Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.
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            Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

            Summary The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.
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              Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

              The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541–750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.
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                Journal
                European Journal of Archaeology
                Eur. j. archaeol
                Cambridge University Press (CUP)
                1461-9571
                1741-2722
                June 17 2021
                : 1-23
                Article
                10.1017/eaa.2021.19
                afd6544d-c6de-4139-83e2-d5c5a8e96e70
                © 2021

                http://creativecommons.org/licenses/by/4.0/

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