Reducing Microbial and Human Contamination in DNA Extractions from Ancient Bones and Teeth

Korlević, Petra; Gerber, Tobias; Gansauge, Marie-Theres; Hajdinjak, Mateja; Nagel, Sarah; Aximu‐Petri, Ayinuer; Meyer, Matthias

doi:10.2144/000114320

Cited by 230 publications

(232 citation statements)

References 39 publications

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“…We took measures to avoid and detect protein contamination throughout our palaeoproteomic workflow. Ancient DNA analysis followed protocols outlined elsewhere (53,54), as did stable isotope and radiocarbon analysis of collagen extracts (55). All biomolecular extractions were performed in dedicated facilities at the Max Planck Institute for Evolutionary Anthropology.…”

Section: Methodsmentioning

confidence: 99%

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

Welker

Hajdinjak

Talamo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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289

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In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.

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Section: Methodsmentioning

confidence: 99%

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

Welker

Hajdinjak

Talamo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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289

260

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“…Bones were sampled using a sterile dentistry drill, and between 15 and 30 mg bone powder was used for DNA extraction, with the exception of Vi-*28, in which three separate parts of the bone were sampled (SI Appendix, Table S3). DNA extraction was performed using a method for ultrashort DNA fragment retrieval (33) with modifications (34). The bone powder of Vi-207 and Vi-208 was treated with 0.5% hypochlorite solution before DNA extraction (34) to remove microbial and modern human DNA contamination.…”

Section: Methodsmentioning

confidence: 99%

“…The bone powder of Vi-207 and Vi-208 was treated with 0.5% hypochlorite solution before DNA extraction (34) to remove microbial and modern human DNA contamination. Next-generation sequencing libraries were prepared from 10 μL of each extract, using two single-stranded library preparation schemes: Vi-207 and Vi-208 with a previously published method (35), with modifications from Korlevi c et al (34), and Vi-*28 with an automated library preparation scheme (36). Libraries were amplified and labeled with a pair of unique index sequences (37,38).…”

Section: Methodsmentioning

confidence: 99%

Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition

Devièse

Karavanić

Comeskey

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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109

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Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000–29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ∼32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative high-performance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe. We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G1, Fd/d+G1 and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G1 and G1–G3. These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.

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“…We extracted 339 DNA [54][55][56] and prepared barcoded next generation sequencing libraries, the majority of which 340…”

Section: Ancient Dna Analysis 338mentioning

confidence: 99%

The Beaker Phenomenon and the Genomic Transformation of Northwest Europe

Olalde

Brace

Allentoft

et al. 2017

Preprint

174

342

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Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900–1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britain’s Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

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Reducing Microbial and Human Contamination in DNA Extractions from Ancient Bones and Teeth

Cited by 230 publications

References 39 publications

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition

The Beaker Phenomenon and the Genomic Transformation of Northwest Europe

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