A5060053271- Forensic and Genetic Research
- Archaeology and ancient environmental studies
- Genomics and Phylogenetic Studies
- Forensic Anthropology and Bioarchaeology Studies
- Oral microbiology and periodontitis research
- Environmental DNA in Biodiversity Studies
- Gut microbiota and health
- Archaeological Research and Protection
- Bacteriophages and microbial interactions
- Molecular Biology Techniques and Applications
- Diverse Musicological Studies
- Dental Radiography and Imaging
- CRISPR and Genetic Engineering
- Hepatitis B Virus Studies
- Salivary Gland Disorders and Functions
- Oral and Maxillofacial Pathology
- Yersinia bacterium, plague, ectoparasites research
- Identification and Quantification in Food
- Marine animal studies overview
- Whipple's Disease and Interleukins
- Dental materials and restorations
- Chromosomal and Genetic Variations
- HIV Research and Treatment
- Single-cell and spatial transcriptomics
- Genetic and phenotypic traits in livestock
Max Planck Institute for the Science of Human History
2019-2024
Friedrich Schiller University Jena
2020-2024
Max Planck Institute for Evolutionary Anthropology
2019-2024
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
2023
Schiller (France)
2023
University of Ferrara
2020
Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities responses. calculus does not typically accumulate as much today historically, clinical research studies focus primarily on living dental biofilm. However, reflect different conditions of the differences in characteristics between sample types have yet been systematically explored. Here, we compare profiles modern plaque, establish expected these...
Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of African hominid oral by analyzing dental biofilms humans and Neanderthals spanning past 100,000 years comparing them with those chimpanzees, gorillas, howler monkeys. identify 10 core bacterial genera that have been maintained within lineage play biofilm structural roles. However, many remain understudied unnamed. find major taxonomic functional...
Abstract Social anthropology and ethnographic studies have described kinship systems networks of contact exchange in extant populations 1–4 . However, for prehistoric societies, these can be studied only indirectly from biological cultural remains. Stable isotope data, sex age at death provide insights into the demographic structure a burial community identify local versus non-local childhood signatures, archaeogenetic data reconstruct relationships between individuals, which enables...
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...
Archaeogenetic time transect in Europe unravels genetic and social changes before after the arrival of “steppe” ancestry.
The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper (CA) settlements were abandoned in favor hilltop sites, and collective graves largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical organization, as exemplified the BA El Argar group. We explored this transition from genomic viewpoint tripling amount data available for period. Concomitant rise starting ~2200 cal BCE, we observe complete...
Significance The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, pathogen’s genetic diversity, geographic spread, transmission dynamics this early period Y. evolution are largely unexplored. Here, we describe a set genomes up to 5,000 y old from across Eurasia. Our data two genetically distinct forms evolved in parallel were both...
Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer pianist, including progressive hearing loss, recurring gastrointestinal complaints, liver disease. In 1802, requested that following death, disease be described made public. Medical biographers have since proposed numerous hypotheses, many substantially heritable conditions. Here we attempt genomic analysis of in order to...
Abstract Human expansion in the course of Neolithic transition western Eurasia has been one major topics ancient DNA research last 10 years. Multiple studies have shown that spread agriculture and animal husbandry from Near East across Europe was accompanied by large-scale human expansions. Moreover, changes subsistence migration associated with hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data Linear Pottery Culture site Derenburg-Meerenstieg II...
Human populations underwent range contractions during the Last Glacial Maximum (LGM) which had lasting and dramatic effects on their genetic variation. The ancestry of individuals associated with post-LGM Magdalenian technocomplex has been interpreted as being derived from groups pre-LGM Aurignacian. However, both these ancestries differ that central European chronologically intermediate Gravettian. Thus, genomic transition pre- to remains unclear also in western Europe, where we lack data...
Condensates formed by complex coacervation are hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into wide range of membraneless compartments. Although RNA is key component biological condensates and central world hypothesis, little known about what determines accumulation in which extend single differ their composition. To address this, we developed an approach read content from synthetic protein-based using...
Sicily is a key region for understanding the agricultural transition in Mediterranean because of its central position. Here, we present genomic and stable isotopic data 19 prehistoric Sicilians covering Mesolithic to Bronze Age periods (10,700-4,100 yBP). We find that Early hunter-gatherers (HGs) from are highly drifted lineage Holocene western European HGs, whereas Late HGs carry ∼20% ancestry related northern (south) eastern indicating substantial gene flow. Neolithic farmers genetically...
Abstract Reverse transcription (RT) is a crucial step in most RNA analysis methods. Optimizing protocols for this initial stage critical effective target detection, particularly when working with limited input RNA. Several factors, such as the material quality and reaction conditions, influence RT efficiency. However, effect of primer length on gene detection efficiency remains largely unknown. Thus, we investigate its impact by generating RNA-seq libraries random primers 6, 12, 18, or 24...
Abstract The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age 1 birthplace earliest steppe pastoralist societies 2 . Yet, despite this region having large influence on subsequent development Europe Asia, questions remain regarding its hunter-gatherer past formation expansionist mobile 3–5 Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find strong genetic differentiation between...
Protocol for the preparation of double-stranded genomic libraries Illumina sequencing, optimised ancient DNA (aDNA) with partial USER enzyme treatment. This protocol generates adapter ligated fragments that can be used in conjunction downstream Indexing protocols. The uracil glycosylase (UDG) (USER enzyme) treatment reduces molecular 'damage' form deaminated cytosines characteristic aDNA interior molecules but leaves this damage on both 5' and 3' ends. is modified after: Rohland et al....
Abstract Southern Italy is a key region for understanding the agricultural transition in Mediterranean due to its central position. We present genomic transect 19 prehistoric Sicilians that covers Early Mesolithic Neolithic period. find hunter-gatherers (HGs) are highly drifted sister lineage Holocene western European HGs, whereas quarter of Late HGs ancestry related from eastern Europe and Near East. This indicates substantial gene flow (south-)eastern between Mesolithic. The farmers...
Abstract The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence pastoralism, horse domestication, and development metallurgy. This study focuses on two north sites sharing Siberian genetic ancestry. One sites, Rostovka, is associated with Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that characterized by elaborate metallurgical objects found throughout Northern Eurasia. profiles Rostovka individuals vary widely along forest-tundra cline...
This protocol converts partially completed double-stranded DNA libraries e.g. from: Non-UDG treated ancient library preparation for Illumina sequencing (dx.doi.org/10.17504/protocols.io.bakricv6) into dual-indexed ready on an platform. Other variants of the above can also be used. includes steps indexing PCR, clean-up, and post-indexing qPCR. is modified after Kircher, M., Sawyer, S. & Meyer, 2012. Double overcomes inaccuracies in multiplex Nucleic acids research, 40(1), p.e3....
This protocol converts partially completed double-stranded DNA libraries e.g. from: Non-UDG treated ancient library preparation for Illumina sequencing (dx.doi.org/10.17504/protocols.io.bakricv6) into dual-indexed ready on an platform. Other variants of the above can also be used. includes steps indexing PCR, clean-up, and post-indexing qPCR. is modified after Kircher, M., Sawyer, S. & Meyer, 2012. Double overcomes inaccuracies in multiplex Nucleic acids research, 40(1), p.e3....
This collection contains established ancient DNA (aDNA) specific protocols for Illumina next generation sequencing. It covers sampling of skeletal remains regions preserving higher amounts aDNA, extraction methods designed retrieval very short fragments, and various library construction (including treatments the 'removal' typical aDNA damage). All have been adapted after published (see each corresponding original publication), are used primarily in Department Archaeogenetics at MPI-SHH...
This protocol describes the amplification procedure of dual-indexed double-stranded DNA libraries, for shotgun Illumina sequencing. It is typically used libraries indexed using following protocol: (https://dx.doi.org/10.17504/protocols.io.bakticwn)
Silica-based total DNA extraction protocol optimised for the recovery of ultra-short molecules from archaeological dental calculus, modified Dabney et al. (2013) PNAS (doi: 10.1073/pnas.1314445110) and adapted calculus by Mann (2018) Scientific Reports https://doi.org/10.1038/s41598-018-28091-9).
Protocol for the preparation of double-stranded genomic libraries Illumina sequencing, optimised ancient DNA (aDNA). This protocol generates adapter ligated fragments that can be used in conjunction with downstream Indexing protocols. does not include UDG (USER) treatment, order to retain molecular 'damage' form deaminated cytosines characteristic aDNA. is modified after Meyer & Kircher (2010) Cold Spring Harb. Protoc. (doi: 10.1101/pdb.prot5448).
This protocol describes how to obtain bone powder from the pars petrosa of disarticulated ossis temporalis, specifically dense parts around cochlea, in a minimally-invasive way by drilling outside. The has been shown consistently yield high amounts aDNA (Pinhasi et al. 2015 PLoS One, doi: 10.1371/journal.pone.0129102).