A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Meyer, Matthias; Kircher, Martin; Gansauge, Marie; Li, Heng; Racimo, Fernando; Mallick, Swapan; Schraiber, Joshua G.; Jay, Flora; Prüfer, Kay; Filippo, Cesare de; Sudmant, Peter H.; Alkan, Can; Fu, Qiaomei; Do, Ron; Rohland, Nadin; Tandon, Arti; Siebauer, Michael; Green, Edward; Bryc, Katarzyna; Briggs, Adrian W.; Stenzel, Udo; Dabney, Jesse; Shendure, Jay; Kitzman, Jacob O.; Hammer, Michael F.; Shunkov, M.V.; Деревянко, А. П.; Patterson, Nick; Andrés, Aida M.; Eichler, Evan E.; Slatkin, Montgomery; Reich, David; Kelso, Janet; Pääbo, Svante

doi:10.1126/science.1224344

Cited by 1,721 publications

(2,020 citation statements)

References 190 publications

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“…This same approach was used in some of the work that showed that chimpanzees (and bonobos) are our closest living relatives. 24,25 P EA , P EM , and P AM are similar to previously defined admixturequantifying statistics, such as D-statistics, 23 E-statistics, 12 enhanced D-statistics, 26 and the D 4P statistic. 11 All of these are counting statistics that condition on the presence or absence of derived alleles across individuals.…”

Section: Allele-sharing Statisticssupporting

confidence: 76%

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

Wall

2017

The American Journal of Human Genetics

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Section: Allele-sharing Statisticssupporting

confidence: 76%

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

Wall

2017

The American Journal of Human Genetics

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“…For all three available Neandertal sequences, this position carries the nucleotide T (34), which translates into the amino acid N (codon "Aat," 3′ to 5′). The position is heterozygous N/D in the Denisovan genome (33), a D in the Ust'-Ishim ∼45,000 BP AMH genome (38), and D in 99.1% of modern humans (32) (codon "Gat," 3′ to 5′). The remaining 0.9% of modern human individuals analyzed match the Neandertal sequence.…”

Section: Resultsmentioning

confidence: 99%

“…We used an error-tolerant search engine (PEAKS) against the human reference proteome and compared our protein sequence data against available amino acid sequence variations known through genomic research for modern humans (32), a Denisovan genome (33), and the coding regions of three Neandertals (34). Using this approach, we confidently identify five proteins that contain a total of seven amino acid positions with nonsynonymous SNPs with both alleles at frequencies ≥1.0% in present-day humans (SI Appendix, Table S6).…”

Section: Resultsmentioning

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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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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“…Briefly, instead of building the libraries exclusively from double-stranded DNA-where only sequences without 'nicks' or single-strand breaks can be incorporated into NGS libraries-the new method first denatures DNA fragments and incorporates the single strands of DNA into NGS libraries, allowing for the recovery of significantly more DNA molecules than hitherto possible. By applying this new method, a 30X coverage genome from the same Denisovan sample [42] and a 54X coverage genome from a female Neanderthal toe bone [31] also from Denisova Cave-known as the Altai Neanderthal-were generated.…”

Section: High-coverage Genomesmentioning

confidence: 99%

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

Sánchez-Quinto

Lalueza-Fox

2015

Phil. Trans. R. Soc. B

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Nearly two decades since the first retrieval of Neanderthal DNA, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a Neanderthal and a Denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the Neanderthal lineage. This genomic information, coupled with diversity exome data from several Neanderthal specimens is shedding new light on evolutionary processes such as the genetic basis of Neanderthal and modern human-specific adaptations-including morphological and behavioural traits-as well as the extent and nature of the admixture events between them. An emerging picture is that Neanderthals had a long-term small population size, lived in small and isolated groups and probably practised inbreeding at times. Deleterious genetic effects associated with these demographic factors could have played a role in their extinction. The analysis of DNA from further remains making use of new large-scale hybridization-capture-based methods as well as of new approaches to discriminate contaminant DNA sequences will provide genetic information in spatial and temporal scales that could help clarify the Neanderthal's-and our very own-evolutionary history.

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A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Cited by 1,721 publications

References 190 publications

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing

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

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

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