A5037816071- Pleistocene-Era Hominins and Archaeology
- Forensic and Genetic Research
- Forensic Anthropology and Bioarchaeology Studies
- Archaeology and ancient environmental studies
- SARS-CoV-2 detection and testing
- Cultural Heritage Materials Analysis
- Conservation Techniques and Studies
- Biosensors and Analytical Detection
- Spacecraft and Cryogenic Technologies
- SARS-CoV-2 and COVID-19 Research
- Statistical Methods and Inference
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Geophysics and Gravity Measurements
- Educational Robotics and Engineering
- Genetic diversity and population structure
- Gamma-ray bursts and supernovae
- Innovative Microfluidic and Catalytic Techniques Innovation
- Chromosomal and Genetic Variations
- COVID-19 diagnosis using AI
- Silicone and Siloxane Chemistry
- Geology and Paleoclimatology Research
- Bacteriophages and microbial interactions
- Metallurgy and Cultural Artifacts
- Environmental DNA in Biodiversity Studies
Max Planck Institute for Evolutionary Anthropology
2017-2024
Max Planck Society
2023-2024
Max Planck Institute for Evolutionary Biology
2023-2024
European Bioinformatics Institute
2023
Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity hominin fossils often impedes understanding which hominins occupied site. Using targeted enrichment mitochondrial DNA, we show that cave sediments represent source ancient mammalian DNA includes traces even at sites and in layers where no remains have been discovered. By automation-assisted screening numerous sediment samples, detected Neandertal eight from four caves Eurasia. In Denisova...
Abstract Modern humans appeared in Europe by at least 45,000 years ago 1–5 , but the extent of their interactions with Neanderthals, who disappeared about 40,000 6 and relationship to broader expansion modern outside Africa are poorly understood. Here we present genome-wide data from three individuals dated between 45,930 42,580 Bacho Kiro Cave, Bulgaria 1,2 . They earliest Late Pleistocene known have been recovered so far, were found association an Initial Upper Palaeolithic artefact...
The value of dirty DNA Environmental can identify the presence species, even from distant past. Surveying three cave sites in western Europe and southern Siberia, Vernot et al. identified nuclear confirmed that it is close relatives anatomically modern humans—Neanderthal Denisovan individuals. A phylogenetic analysis modeling show sediment samples several layers corresponds to previously studied skeletal remains. These results demonstrate environmental data be applied study population...
Denisova Cave in southern Siberia is the type locality of Denisovans, an archaic hominin group who were related to Neanderthals1-4. The dozen remains recovered from deposits also include Neanderthals5,6 and child a Neanderthal Denisovan7, which suggests that was contact zone between these hominins. However, uncertainties persist about order groups appeared at site, timing environmental context occupation, association particular with archaeological assemblages5,8-11. Here we report analysis...
Abstract Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans 1–8 , but the social organization Neanderthal communities remains poorly understood. Here we present genetic data for 13 from two Middle Palaeolithic sites in Altai Mountains southern Siberia: 11 Chagyrskaya Cave 9,10 2 Okladnikov —making this one largest studies a date. We used hybridization capture obtain genome-wide nuclear data, as well mitochondrial...
The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and spread Homo sapiens. Late persisted western several millennia after occurrence H. sapiens eastern
Y chromosome evolution in Neanderthals The genomes of archaic hominins have been sequenced and compared with that modern humans. However, most individuals high-quality sequences available female. Petr et al. performed targeted sequencing the paternally inherited chromosomes from three two Denisovans (see Perspective by Schierup). Comparisons diverse human indicated that, similar to maternally mitochondria, Neanderthal were more closely related each other Denisovan chromosome. This result...
Significance DNA preserved in sediments has emerged as an important source of information about past ecosystems, independent the discovery skeletal remains. However, little is known sources sediment DNA, factors affecting its long-term preservation, and extent to which it may be translocated after deposition. Here, we show that impregnated blocks intact are excellent archives DNA. distribution highly heterogeneous at microscale cave studied, suggesting postdepositional movement unlikely a...
Abstract Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour culture in the Pleistocene. Although these resources plentiful, it is impossible associate artefacts specific individuals 1 who can be morphologically or genetically characterized, unless they found within burials, which rare this time period. Thus, ability discern societal roles Pleistocene based on their biological sex genetic ancestry limited 2–5 . Here we...
Little is known about the population history of Neandertals over hundreds thousands years their existence. We retrieved nuclear genomic sequences from two Neandertals, one Hohlenstein-Stadel Cave in Germany and other Scladina Belgium, who lived around 120,000 ago. Despite deeply divergent mitochondrial lineage present former individual, both are genetically closer to later Europe than a roughly contemporaneous individual Siberia. That individuals time most recent common ancestor with...
The Forbes’ Quarry and Devil’s Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA preserved in petrous bones 2 individuals despite unfavorable climatic conditions. However, endogenous is present an overwhelming excess recent human DNA. Using improved library construction methods enrich for fragments carrying deaminated cytosine residues, were able to sequence 70 0.4 megabase pairs (Mbp) nuclear specimens,...
SARS-CoV-2 causes substantial morbidity and mortality in elderly immunocompromised individuals, particularly retirement homes, where transmission from asymptomatic staff visitors may introduce the infection. Here we present a cheap fast screening method based on direct RT-qPCR to detect single or pooled gargle lavages ("mouthwashes"). This detects individuals with large viral loads (Ct≤29) use it test all at nursing home daily over period of three weeks order reduce risk that infection...
Abstract Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans 1–8 , but the social organization Neanderthal communities remains poorly understood. Here, we present genetic data for 13 from two Middle Palaeolithic sites in Altai Mountains southern Siberia: 11 Chagyrskaya Cave 9,10 Okladnikov - making this largest study a date. We used hybridization capture obtain genome-wide nuclear data, as well mitochondrial...
Abstract SARS-CoV-2 causes substantial morbidity and mortality in elderly immunocompromised individuals, particularly retirement homes, where transmission from asymptomatic staff visitors may introduce the infection. Here we present a cheap fast approach to detect single or pooled gargle lavages (“mouthwashes”). With this approach, test all at nursing home daily over period of three weeks order reduce risk that infection penetrates facility. This similar approaches could be implemented...
Contamination with microbial and other exogenous DNA poses a significant challenge in the generation of genome-wide sequence data from ancient skeletal remains. Here we describe method for separating into multiple fractions during extraction by sequential temperature-controlled release sodium phosphate buffer. An evaluation effectiveness using set three bones resulted between 1.6- 32-fold enrichment endogenous compared regular extraction. For two bones, outperformed previous methods...
Protocol for reducing DNA contamination on materials (e.g. quarz glass bottles, spatulas) used in the ancient cleanroom by sodium hypochlorite (bleach) and UV treatment.
Protocol for the preparation of 0.1x BWT+SDS buffer (Bind and wash I) automated single-stranded DNA library using ssDNA2.0 method (Gansauge et al. 2020). References Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meyer, M. (2020). Manual libraries sequencing from ancient biological remains other sources highly degraded DNA. Nature Protocols, 15, 2279-2300.
Protocol for the preparation of 0.1x BWT+SDS buffer (Bind and wash I) automated single-stranded DNA library using ssDNA2.0 method (Gansauge et al. 2020). References Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meyer, M. (2020). Manual libraries sequencing from ancient biological remains other sources highly degraded DNA. Nature Protocols, 15, 2279-2300.
We here provide a protocol for automated hybridization capture of ancient DNA libraries on the Hamilton NGS Star in 96-well format using method originally developed by Gnirke et al. 2009 and modified at MPI-EVA use with Fu 2013. Modifications to latter include omission wash Wash Buffer 3 hydroxide melt step elution captured library molecules prior amplification. In-solution is performed single-stranded biotinylated probes, which can be generated from oligonucleotide arrays, synthetic pools...
We here provide a protocol for the decontamination of ancient bones and teeth that is based on temperature-controlled, sequential release DNA. DNA can be extracted from all fractions generated with this method fraction highest proportion endogenous identified further analysis. The proceeds through repeated incubation sample powder in phosphate buffer at 37, 60 90 °C, followed by complete lysis residual powder. As denatured high temperature, subsequent extraction library preparation has to...
Protocol for reducing DNA contamination of reagents and buffers used in the ancient cleanroom by UV treatment. Change log: small formatting edits (20240111, EE) language consistency (20240123,
Protocol for reducing DNA contamination on tubes, bottles, zip lock bags and other reaction vessels containers used in the ancient cleanroom by UV treatment. Change log: Formatting edits consistency with documents/protocols (20240110, EE)
We here provide an implementation of the ssDNA2.0 single-stranded library preparation method (Gansauge et al. 2017, Gansauge 2020) for automated liquid handling on Bravo NGS workstation B in 96-well format. The was developed primarily ancient DNA research but is also suitable from other sources degraded or DNA, such as cell-free formalin-fixed samples synthetic oligonucleotides. To use protocol, a required. Calibration instrument this protocol has to be performed by user and requires...
We here provide a protocol for the simultaneous amplification and dual-indexing of 96 DNA libraries through automated liquid handling using Bravo NGS workstation (Agilent Technologies). The benefits preventing detecting cross-contamination have been documented elsewhere (Kircher et al. 2012, Zavala 2022). This is optimized specifically ancient degraded (i.e., with short inserts) compatible both double- single-stranded methods preparing Illumina-type (e.g., Meyer Kircher 2010, Gansauge 2020)....