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Harbeck M.,State Collection for Anthropology and Palaeoanatomy | Seifert L.,Ludwig Maximilians University of Munich | Hansch S.,Johannes Gutenberg University Mainz | Hansch S.,University of Oslo | And 13 more authors.
PLoS Pathogens | Year: 2013

Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19th and 20th centuries, during which plague was spread around the world, and the second pandemic of the 14th-17th centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6th-8th centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics. © 2013 Harbeck et al.


Wagner D.M.,Northern Arizona University | Klunk J.,McMaster University | Harbeck M.,State Collection for Anthropology and Palaeoanatomy | Devault A.,McMaster University | And 25 more authors.
The Lancet Infectious Diseases | Year: 2014

Background: Yersinia pestis has caused at least three human plague pandemics. The second (Black Death, 14-17th centuries) and third (19-20th centuries) have been genetically characterised, but there is only a limited understanding of the first pandemic, the Plague of Justinian (6-8th centuries). To address this gap, we sequenced and analysed draft genomes of Y pestis obtained from two individuals who died in the first pandemic. Methods: Teeth were removed from two individuals (known as A120 and A76) from the early medieval Aschheim-Bajuwarenring cemetery (Aschheim, Bavaria, Germany). We isolated DNA from the teeth using a modified phenol-chloroform method. We screened DNA extracts for the presence of the Y pestis-specific pla gene on the pPCP1 plasmid using primers and standards from an established assay, enriched the DNA, and then sequenced it. We reconstructed draft genomes of the infectious Y pestis strains, compared them with a database of genomes from 131 Y pestis strains from the second and third pandemics, and constructed a maximum likelihood phylogenetic tree. Findings: Radiocarbon dating of both individuals (A120 to 533 AD [plus or minus 98 years]; A76 to 504 AD [plus or minus 61 years]) places them in the timeframe of the first pandemic. Our phylogeny contains a novel branch (100% bootstrap at all relevant nodes) leading to the two Justinian samples. This branch has no known contemporary representatives, and thus is either extinct or unsampled in wild rodent reservoirs. The Justinian branch is interleaved between two extant groups, 0.ANT1 and 0.ANT2, and is distant from strains associated with the second and third pandemics. Interpretation: We conclude that the Y pestis lineages that caused the Plague of Justinian and the Black Death 800 years later were independent emergences from rodents into human beings. These results show that rodent species worldwide represent important reservoirs for the repeated emergence of diverse lineages of Y pestis into human populations. Funding: McMaster University, Northern Arizona University, Social Sciences and Humanities Research Council of Canada, Canada Research Chairs Program, US Department of Homeland Security, US National Institutes of Health, Australian National Health and Medical Research Council. © 2014 Elsevier Ltd.


Olsen K.C.,University of Western Ontario | White C.D.,University of Western Ontario | Longstaffe F.J.,University of Western Ontario | Von Heyking K.,Ludwig Maximilians University of Munich | And 3 more authors.
American Journal of Physical Anthropology | Year: 2014

Paleodiet research traditionally interprets differences in collagen isotopic compositions (δ13C, δ15N) as indicators of dietary distinction even though physiological processes likely play some role in creating variation. This research investigates the degree to which bone collagen δ13C and δ15N values normally vary within the skeleton and examines the influence of several diseases common to ancient populations on these isotopic compositions. The samples derive from two medieval German cemeteries and one Swiss reference collection and include examples of metabolic disease (rickets/osteomalacia), degenerative joint disease (osteoarthritis), trauma (fracture), infection (osteomyelitis), and inflammation (periostitis). A separate subset of visibly nonpathological skeletal elements from the German collections established normal intraindividual variation. For each disease type, tests compared bone lesion samples to those near and distant to the lesions sites. Results show that normal (nonpathological) skeletons exhibit limited intraskeletal variation in carbon- and nitrogen-isotope ratios, suggesting that sampling of distinct elements is appropriate for paleodiet studies. In contrast, individuals with osteomyelitis, healed fractures, and osteoarthritis exhibit significant intraskeletal differences in isotope values, depending on whether one is comparing lesions to near or to distant sites. Skeletons with periostitis result in significant intraskeletal differences in nitrogen isotope values only, while those with rickets/osteomalacia do not exhibit significant intraskeletal differences. Based on these results, we suggest that paleodiet researchers avoid sampling collagen at or close to lesion sites because the isotope values may be reflecting both altered metabolic processes and differences in diet relative to others in the population. Am J Phys Anthropol 153:598-604, 2014. © 2013 Wiley Periodicals, Inc. Copyright © 2013 Wiley Periodicals, Inc.


Keller M.,Ludwig Maximilians University of Munich | Rott A.,State Collection for Anthropology and Palaeoanatomy | Hoke N.,Ludwig Maximilians University of Munich | Schwarzberg H.,Bavarian State Archaeological Collection | And 3 more authors.
American Journal of Physical Anthropology | Year: 2015

Objectives: Straight next to a segment of the outer ditch of the Late Neolithic Michelsberg Culture earthwork of Bruchsal-Aue in SW-Germany (ca. 4250-3650 calBC), a multiple burial of eight individuals (two male adults and six children) plus a subsequent child burial was excavated. In this study, we applied a multidisciplinary approach to elucidate interpersonal relationships and life histories within this collective. Materials and methods: To determine the identity of this collective, we performed aDNA analyses in addition to osteological examination using HVR I plus Y-chromosomal and autosomal STR profiling to find evidence for kinship relations. Strontium isotopic analyses were used to reconsider migrational behavior. To find evidence for a specific social affiliation, the individual diet was reconstructed by performing nitrogen and carbon isotopic analyses. Furthermore, radiocarbon-dating was carried out to integrate the burial context into an absolute timeframe. Two nearby single burials were included in the analyses for comparison. Results: Because of a shared HVR I haplotype, three pairs of individuals were most likely linked by kinship, and statistical testing on autosomal STR profiles shows a high probability for the pair of two men being brothers. Although it cannot be excluded, isotopic data gave no clear proof for migration. A rather poor health status is indicated by skeletal stress markers even though the isotope data attest to a diet rich in meat and fish. Discussion: Although clear kinship relations among the infants remain unconfirmed, a relationship could also be indicated by the positioning of the bodies in the burial pit. Whereas a common cause of death might have been the presupposition for their special treatment, interpersonal relationships were likely the decisive factor for the multiple burial. © 2015 Wiley Periodicals, Inc.


PubMed | Ludwig Maximilians University of Munich, Bavarian State Archaeological Collection, State Office for Cultural Heritage Management Baden Wurttemberg and State Collection for Anthropology and Palaeoanatomy
Type: Journal Article | Journal: American journal of physical anthropology | Year: 2015

Straight next to a segment of the outer ditch of the Late Neolithic Michelsberg Culture earthwork of Bruchsal-Aue in SW-Germany (ca. 4250-3650 calBC), a multiple burial of eight individuals (two male adults and six children) plus a subsequent child burial was excavated. In this study, we applied a multidisciplinary approach to elucidate interpersonal relationships and life histories within this collective.To determine the identity of this collective, we performed aDNA analyses in addition to osteological examination using HVR I plus Y-chromosomal and autosomal STR profiling to find evidence for kinship relations. Strontium isotopic analyses were used to reconsider migrational behavior. To find evidence for a specific social affiliation, the individual diet was reconstructed by performing nitrogen and carbon isotopic analyses. Furthermore, radiocarbon-dating was carried out to integrate the burial context into an absolute timeframe. Two nearby single burials were included in the analyses for comparison.Because of a shared HVR I haplotype, three pairs of individuals were most likely linked by kinship, and statistical testing on autosomal STR profiles shows a high probability for the pair of two men being brothers. Although it cannot be excluded, isotopic data gave no clear proof for migration. A rather poor health status is indicated by skeletal stress markers even though the isotope data attest to a diet rich in meat and fish.Although clear kinship relations among the infants remain unconfirmed, a relationship could also be indicated by the positioning of the bodies in the burial pit. Whereas a common cause of death might have been the presupposition for their special treatment, interpersonal relationships were likely the decisive factor for the multiple burial.


Seifert L.,Ludwig Maximilians University of Munich | Wiechmann I.,Ludwig Maximilians University of Munich | Harbeck M.,State Collection for Anthropology and Palaeoanatomy | Thomas A.,Ludwig Maximilians University of Munich | And 6 more authors.
PLoS ONE | Year: 2016

Ancient DNA (aDNA) recovered from plague victims of the second plague pandemic (14th to 17th century), excavated from two different burial sites in Germany, and spanning a time period of more than 300 years, was characterized using single nucleotide polymorphism (SNP) analysis. Of 30 tested skeletons 8 were positive for Yersinia pestis-specific nucleic acid, as determined by qPCR targeting the pla gene. In one individual (MP-19-II), the pla copy number in DNA extracted from tooth pulp was as high as 700 gene copies/μl, indicating severe generalized infection. All positive individuals were identical in all 16 SNP positions, separating phylogenetic branches within nodes N07-N10 (14 SNPs), N07-N08 (SNP s19) and N06-N07 (s545), and were highly similar to previously investigated plague victims from other European countries. Thus, beside the assumed continuous reintroduction of Y. pestis from central Asia in multiple waves during the second pandemic, long-term persistence of Y. pestis in Europe in a yet unknown reservoir host has also to be considered. © 2016 Seifert et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Seifert L.,Ludwig Maximilians University of Munich | Harbeck M.,State Collection for Anthropology and Palaeoanatomy | Thomas A.,University of Federal Defense Munich | Hoke N.,Ludwig Maximilians University of Munich | And 5 more authors.
PLoS ONE | Year: 2013

Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14th century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the Y. pestis specific pla gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both Y. pestis specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 Y. pseudotuberculosis strains as well as for DNA of 22 Y. pestis strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per μl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study. © 2013 Seifert et al.


Hoke N.,Ludwig Maximilians University of Munich | Grigat A.,State Collection for Anthropology and Palaeoanatomy | Grupe G.,Ludwig Maximilians University of Munich | Harbeck M.,State Collection for Anthropology and Palaeoanatomy
Forensic Science International | Year: 2013

Assessing the UV-fluorescence of a freshly cut cross section of the compact parts of a bone is often recommended as a first step to estimate the postmortem interval (PMI) of skeletal remains. Opinions differ concerning the cause of fluorescence and on how to categorize fluorescent properties as well as the significance of fluorescent characteristics in correlation with the PMI. In this study we evaluated the UV-fluorescence of over 200 bones with known PMI to reassess the diagnostic value of this method for differentiating between historical and recent skeletal remains. It could be shown that there is a correlation between the PMI and fluorescence colour, but not with fluorescence intensity. Furthermore, the quality of two UV-fluorescence test possibilities based on fluorescence colour was assessed by calculating the individual test efficiency, sensitivity and specificity. The results showed that blue bone fluorescence, as well as blue fluorescence combined with other colours (mainly yellow) does not allow the observer to draw any conclusions about sample age. Only overall yellow fluorescence may indicate a historical specimen. But still, 2% of all forensically relevant samples were falsely excluded, making bone fluorescent properties inappropriate as the sole criterion for deciding whether a specimen is included or excluded for further forensic investigation. © 2013 Elsevier Ireland Ltd.

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