A5051221853- Yersinia bacterium, plague, ectoparasites research
- Forensic and Genetic Research
- Bacillus and Francisella bacterial research
- Archaeology and ancient environmental studies
- Forensic Anthropology and Bioarchaeology Studies
- Genomics and Phylogenetic Studies
- Amino Acid Enzymes and Metabolism
- Bacterial Identification and Susceptibility Testing
- Leprosy Research and Treatment
- Mycobacterium research and diagnosis
- Historical and Archaeological Studies
- Zoonotic diseases and public health
- Ancient and Medieval Archaeology Studies
- Paleopathology and ancient diseases
- Vector-borne infectious diseases
- Hepatitis B Virus Studies
- Bacterial Genetics and Biotechnology
- HIV Research and Treatment
- Indigenous Studies and Ecology
- Genetic diversity and population structure
- Escherichia coli research studies
- Hepatitis C virus research
- Animal Diversity and Health Studies
- Historical Studies and Socio-cultural Analysis
- Pleistocene-Era Hominins and Archaeology
University of Tartu
2019-2023
Estonian Biocentre
2020-2023
University of Bern
2021-2023
University of Cambridge
2021-2023
Max Planck Institute for the Science of Human History
2016-2021
Bavarian Natural History Collections
2019
Ludwig-Maximilians-Universität München
2015-2018
Bavarian State Collection of Zoology
2016-2018
Max Planck Society
2017
Abstract Domestication of horses fundamentally transformed long-range mobility and warfare 1 . However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence bridling, milking corralling 2–4 at Botai, Central Asia around 3500 bc 3 Other longstanding candidate regions for domestication, such as Iberia 5 Anatolia 6 , have also recently been challenged. Thus, genetic, geographic temporal origins remained unknown. Here we...
Abstract The second plague pandemic, caused by Yersinia pestis , devastated Europe and the nearby regions between 14 th 18 centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period reconstruct 34 ancient Y. genomes. Our data support an initial entry of bacterium through eastern Europe, absence genetic diversity during Black Death, low within-outbreak thereafter. Analysis post-Black Death genomes shows diversification a lineage into multiple...
The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within Roman Empire and continued so-called First Pandemic until 750. Although paleogenomic studies have previously identified causative agent Y. pestis, little is known about bacterium's spread, diversity, genetic history over course of pandemic. To elucidate microevolution bacterium during this time period, we screened human remains from 21 sites Austria, Britain, Germany, France,...
The Justinianic Plague, which started in the sixth century and lasted to mid eighth century, is thought be first of three historically documented plague pandemics causing massive casualties. Historical accounts molecular data suggest bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. genome obtained from sixth-century skeleton recovered southern German burial site close Munich. reconstructed enabled detection 30 unique substitutions well...
Ancient DNA traces the history of hepatitis B Hepatitis virus (HBV) infections represent a worldwide human health concern. To study this pathogen, Kocher et al . identified 137 remains with detectable levels dating between 400 and 10,000 years ago. Sequencing analyses these ancient viruses suggested common ancestor 12,000 20,000 There is no evidence indicating that HBV was present in earliest humans as they spread out Africa; however, likely populations before farming. Furthermore, Americas...
Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history appearance historical records, origins past dissemination patterns are still widely unknown. Applying ancient DNA approaches to major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic...
The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major worldwide infant mortality before introduction vaccine 1980s. Although occurrence serotype b (Hib), most virulent type H. influenzae, has since decreased, reports infections with other serotypes non-typeable strains are on rise. While have been studied in-depth, very little is known pathogen's evolutionary history, no genomes dating prior to 1940 were available.
Ancient DNA from Yersinia pestis has been identified in skeletons at four urban burial grounds Cambridge, England, and a nearby rural cemetery. Dating to between ad 1349 1561, these represent individuals who died of plague during the second pandemic. Most come normative individual burials, rather than mass graves. This pattern represents major advance archaeological knowledge, shifting focus away few exceptional discoveries burials what was normal practice most medieval contexts. Detailed...
Abstract Although dozens of ancient Yersinia pestis genomes and a vast corpus documentary data are available, the origin spread consecutive outbreaks Second Plague Pandemic in Europe (14th–18th c.) still poorly understood. For majority genomes, only radiocarbon dates spanning several decades hampering an association with historically recorded plague outbreaks. Here, we present new genomic evidence from 11 sites England, Estonia, Netherlands, Russia, Switzerland yielding Y. >4-fold mean...
Zoonoses are among the greatest threats to human health, with many zoonotic pathogens believed have emerged during prehistory. Palaeomicrobiological investigations of zooarchaeological record hold potential uncover reservoirs, host ranges, and adaptations but face challenges in identifying promising specimens pathogen DNA preservation. We performed palaeopathological genetic examinations 346 skeletal elements from domesticated wild animals collected 34 Eurasian sites dating across last six...
Abstract Objectives Warfare is assumed to be one of the defining cultural characteristics steppe nomads in Eastern Eurasia. For first‐centuries CE, a period political turmoil Northern China and Southern Siberia, relatively few data are, however, available about degree variability violence these communities. Here, we provide new on among during CE by analyzing type, anatomical distribution, demographic distribution perimortem trauma at Tunnug1 (Tuva, Siberia—second fourth c. CE). Materials...
DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, performance of hyRAD as an inexpensive and design-free alternative commercial capture protocols obtain authentic aDNA data from osseous remains. HyRAD relies double enzymatic restriction fresh...
Objectives: Straight next to a segment of the outer ditch Late Neolithic Michelsberg Culture earthwork Bruchsal-Aue in SW-Germany (ca. 4250–3650 calBC), multiple burial eight individuals (two male adults and six children) plus subsequent child was excavated. In this study, we applied multidisciplinary approach elucidate interpersonal relationships life histories within collective. Materials methods: To determine identity collective, performed aDNA analyses addition osteological examination...
The Middle and Late Bronze Age, a period roughly spanning the 2 nd millennium BC (ca. 2000–1200 BC) in Near East, is frequently referred to as first ‘international age’, characterized by intense far-reaching contacts between different entities from eastern Mediterranean East beyond. In large-scale tandem study of stable isotopes ancient DNA individuals excavated at Tell Atchana (Alalakh, located Hatay, Turkey), we explored role mobility capital regional kingdom, named Mukish during which...
Abstract Objectives Contemporary archeological theory emphasizes the economic and social complexity of Eurasian steppe populations. As a result, old notions “nomadic” cultures as homogenously mobile economically simple are now displaced by more nuanced interpretations. Large part literature on diet mobility among pastoralists is focused Bronze Iron Ages. The underrepresentation recent contexts hampers full discussion possible chronological trajectories. In this study we explore at Tunnug1...
Zusammenfassung: Vergangene Pestepidemien wurden vor allem in schriftlichen Quellen überliefert; insbesondere die Justinianische Pest des frühen Mittelalters und der Schwarze Tod späten dort lebendigen Farben beschrieben. Vor Einführung aDNA-Analyse war es aber oftmals schwierig, archäologische nachgewiesene Bestattungen eindeutig zuzuweisen – Gegenden, wo schriftliche Überlieferungen, erwähnen, fehlen. Die Analyse alter DNA erlaubt nun, Opfer im archäologischen Befund zu identifizieren. In...
Abstract Along with the publication of 137 ancient human genomes retrieved from archaeological remains Eurasian steppe, Damgaard et al., 2018 identified two individuals infected Yersinia pestis , yielding one genome 0.24x average coverage (DA147, 6 th –9 c. AD) and another 8.7x (DA101, 2 nd –3 rd AD). A phylogenetic analysis performed on latter placed it in a position ancestral to -century Justinianic Aschheim, Germany. These results are used fuel an argument that Plague (541–544 “was...
Abstract Of all known epidemics in Antiquity, the Justinianic Plague became focus of attention recent years - not least because it is first for which causative agent, bacterium Yersinia pestis, could be unambiguously identified by palaeogeneticists. The reconstruction ancient Y. pestis genomes able to uncover geographical and temporal extent pandemic beyond limitations written sources; phylogenetic studies allow inferences on origin spread plague through time. But even mere identification...
Protocol for the purification of extracts, modified from Dabney et al. (2013) PNAS (doi: 10.1073/pnas.1314445110).
Protocol for the preparation of double indexed double-stranded DNA libraries Illumina sequencing, optimized ultra-short ancient molecules, modified from Meyer & Kircher (2010) Cold Spring Harb. Protoc. (doi: 10.1101/pdb.prot5448). This protocol does include treatment with UDG (USER) to remove damage in form deaminated cytosines.
Protocol for the preparation of single indexed double-stranded DNA libraries Illumina sequencing, optimized ultra-short ancient molecules, modified from Meyer & Kircher (2010) Cold Spring Harb. Protoc. (doi: 10.1101/pdb.prot5448). This protocol does not include treatment with UDG (USER) to remove damage in form deaminated cytosines.
The second plague pandemic (14th - 18th century AD), caused by the bacterium Yersinia pestis , is infamous for its initial wave, Black Death (1346-1353 and repeated scourges in Europe vicinity until Early Modern Era. Here, we report 32 ancient Y. genomes spanning 14th to 17th AD through analysis of human remains from nine European archaeological sites. Our data support an entry Eastern absence genetic diversity during as well low local outbreaks thereafter. Moreover, post-Black shows...
Abstract The first historically documented pandemic caused by Yersinia pestis started as the Justinianic Plague in 541 within Roman Empire and continued so-called First Pandemic until 750. Although palaeogenomic studies have previously identified causative agent Y. , little is known about bacterium’s spread, diversity genetic history over course of pandemic. To elucidate microevolution bacterium during this time period, we screened human remains from 20 sites Austria, Britain, Germany,...
Protocol for the indexing PCR and purification of dsDNA libraries, optimized ultra-short ancient DNA molecules, modified from Meyer & Kircher (2010) Cold Spring Harb. Protoc. (doi: 10.1101/pdb.prot5448).
Protocol for the preparation of single indexed double-stranded DNA libraries Illumina sequencing, optimized ultra-short ancient molecules, modified from Meyer & Kircher (2010) Cold Spring Harb. Protoc. (doi: 10.1101/pdb.prot5448). This protocol does include treatment with UDG (USER) to remove damage in form deaminated cytosines.