The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
Open accessAbstract
One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation-summarized in a postmortem degradation score-which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“By characterizing damage patterns, users can distinguish authentic aDNA from modern contaminants, thereby ensuring the integrity of the dataset (Jónsson et al. 2013, Skoglund et al. 2014).”
From Unravelling reference bias in ancient DNA datasets (2024) · cites this paper as Skoglund et al. 2014
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Cytosine deamination can also be estimated using the tool PMDtools 55 on data generated following full USER-treatment by conditioning on CpG dinucleotides 125 , since these are heavily methylated in the nuclear genomes of vertebrates and protected from USER degradation.”
From Ancient DNA analysis (2021) · cites this paper as [55]
The cited source says what the claim attributes to it.
In the citing paper
“For highly degraded or contaminated material, analyses may be conditioned on reads showing evidence of post-mortem DNA damage 55,189,192 and/or limited to transversions 7 so as to mitigate both rampant contamination and damage-related nucleotide misincorporation.”
From Ancient DNA analysis (2021) · cites this paper as [55]
The cited source says what the claim attributes to it.
In the citing paper
“The list of factors to consider extends far beyond the minimal data requirement for specific analyses 330 and includes: platform-specific sequence error profiles 169 ; the magnitude of post-mortem DNA damage and contamination and their impact on downstream inference 55 ; base quality rescaling 57 ; read alignment parameters 180,182 ; database selection and taxonomic classifier parameters 27,238 ;”
From Ancient DNA analysis (2021) · cites this paper as [55]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A. E., Höhna, S., Larget, B. R., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys029 · Cited by 28,399
Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Humana Press eBooks · doi:10.1385/1-59259-192-2:365 · Cited by 15,068
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318
Integrating common and rare genetic variation in diverse human populations
The International HapMap 3 Consortium (2010) · Nature · doi:10.1038/nature09298 · Cited by 3,026
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and SequencingPreprint
Meyer, M., & Kircher, M. (2010) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot5448 · Cited by 2,233
Genetic history of an archaic hominin group from Denisova Cave in Siberia
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991
Self-citationA high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967
Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., Cann, H. M., Barsh, G. S., Feldman, M. W., Cavalli-Sforza, L. L., et al. (2008) · Science · doi:10.1126/science.1153717 · Cited by 1,915
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F., & Orlando, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt193 · Cited by 1,669
Mitochondrial genome variation and the origin of modern humans
Ingman, M., Kaessmann, H., Pääbo, S., & Gyllensten, U. B. (2000) · Nature · doi:10.1038/35047064 · Cited by 1,546
Neandertal DNA Sequences and the Origin of Modern Humans
Krings, M., Stone, A. C., Schmitz, R. W., Krainitzki, H., Stoneking, M., & Pääbo, S. (1997) · Cell · doi:10.1016/s0092-8674(00)80310-4 · Cited by 1,339
Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.
Pääbo, S. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.6.1939 · Cited by 1,020
Patterns of damage in genomic DNA sequences from a neandertal
Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704665104 · Cited by 981
Ancient human genome sequence of an extinct Palaeo-Eskimo
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., et al. (2010) · Nature · doi:10.1038/nature08835 · Cited by 849
The complete mitochondrial DNA genome of an unknown hominin from southern Siberia
Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010) · Nature · doi:10.1038/nature08976 · Cited by 818
An aboriginal Australian genome reveals separate human dispersals into Asia
Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., et al. (2011) · Science · doi:10.1126/science.1211177 · Cited by 787
Analysis of one million base pairs of Neanderthal DNA
Green, R. E., Krause, J., Ptak, S. E., Briggs, A. W., Ronan, M. T., Simons, J. F., Du, L., Egholm, M., Rothberg, J. M., Paunović, M., et al. (2006) · Nature · doi:10.1038/nature05336 · Cited by 758
Hofreiter, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4793 · Cited by 684
Sequencing and analysis of Neanderthal genomic DNA
Noonan, J. P., Coop, G., Kudaravalli, S., Smith, D., Krause, J., Alessi, J., Chen, F., Platt, D., Pääbo, S., Pritchard, J. K., et al. (2006) · Science · doi:10.1126/science.1131412 · Cited by 629
Self-citationA Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing
Green, R. E., Malaspinas, A., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maričić, T., Stenzel, U., et al. (2008) · Cell · doi:10.1016/j.cell.2008.06.021 · Cited by 608
DNA analysis of an early modern human from Tianyuan Cave, China
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221359110 · Cited by 608 · cited 5×
“We used the calmd program in the samtools (6) suite to recompute the MD field (containing alignment information, such as mismatches) for all datasets.”
MethodInfluentialMolecular analysis of Neanderthal DNA from the northern Caucasus
Ovchinnikov, I. V., Götherström, A., Romanova, G. P., Kharitonov, V. M., Lidén, K., & Goodwin, W. (2000) · Nature · doi:10.1038/35006625 · Cited by 550
Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P., Willerslev, E., Gilbert, M. T. P., Götherström, A., & Jakobsson, M. (2012) · Science · doi:10.1126/science.1216304 · Cited by 521
Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes
Briggs, A. W., Good, J. M., Green, R. E., Krause, J., Maričić, T., Stenzel, U., Lalueza‐Fox, C., Rudan, P., Brajković, D., Kućan, Ž., et al. (2009) · Science · doi:10.1126/science.1174462 · Cited by 508
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034131 · Cited by 489
Self-citationNew insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
Keller, A., Graefen, A., Ball, M., Matzas, M., Boisguerin, V., Maixner, F., Leidinger, P., Backes, C., Khairat, R., Forster, M., et al. (2012) · Nature Communications · doi:10.1038/ncomms1701 · Cited by 437
Comparison and Optimization of Ancient DNA Extraction
Rohland, N., & Hofreiter, M. (2007) · BioTechniques · doi:10.2144/000112383 · Cited by 371
A view of Neandertal genetic diversity
Krings, M., Capelli, C., Tschentscher, F., Geisert, H., Meyer, S., von Haeseler, A., Großschmidt, K., Possnert, G., Paunović, M., & Pääbo, S. (2000) · Nature Genetics · doi:10.1038/79855 · Cited by 339
Neanderthals in central Asia and Siberia
Krause, J., Orlando, L., Serre, D., Viola, B., Prüfer, K., Richards, M. P., Hublin, J.-J., Hänni, C., Derevianko, A. P., & Pääbo, S. (2007) · Nature · doi:10.1038/nature06193 · Cited by 333
Self-citationThe retrieval of ancient human DNA sequences.
Handt, O., Krings, M., Ward, R. H., & Pääbo, S. (1996) · PubMed · Cited by 325
Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts
Gilbert, M. T. P., Tomsho, L. P., Rendulic, S., Packard, M., Drautz, D. I., Sher, A. V., Tikhonov, A., Dalén, L., Kuznetsova, T. V., Kosintsev, P. A., et al. (2007) · Science · doi:10.1126/science.1146971 · Cited by 277
Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Kircher, M., Stenzel, U., & Kelso, J. F. (2009) · Genome biology · doi:10.1186/gb-2009-10-8-r83 · Cited by 271
Brotherton, P., Endicott, P., Sánchez, J. J. M., Beaumont, M., Barnett, R., Austin, J. J., & Cooper, A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm588 · Cited by 261
A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia
Krause, J., Briggs, A. W., Kircher, M., Maricic, T., Zwyns, N., Derevianko, A., & Pääbo, S. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.068 · Cited by 259
Analysis of High-Throughput Ancient DNA Sequencing Data
Kircher, M. (2012) · Methods in Molecular Biology · doi:10.1007/978-1-61779-516-9_23 · Cited by 236
Learning about human population history from ancient and modern genomes
Stoneking, M., & Krause, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3029 · Cited by 215
The neandertal genome and ancient DNA authenticity
Green, R. E., Briggs, A. W., Krause, J., Prüfer, K., Burbano, H. A., Siebauer, M., Lachmann, M., & Pääbo, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.222 · Cited by 190
Statistical Evidence for Miscoding Lesions in Ancient DNA Templates
Hansen, A. J., Willerslev, E., Wiuf, C., Mourier, T., & Arctander, P. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003800 · Cited by 184
Inconsistencies in Neanderthal Genomic DNA Sequences
Wall, J. D., & Kim, S. K. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030175 · Cited by 181
Extensive Human DNA Contamination in Extracts from Ancient Dog Bones and Teeth
Malmström, H., Storå, J., Dalén, L., Holmlund, G., & Götherström, A. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi195 · Cited by 175
Archaic human ancestry in East Asia
Skoglund, P., & Jakobsson, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1108181108 · Cited by 170
Authenticating DNA Extracted From Ancient Skeletal Remains
Richards, M. B., Sykes, B. C., & Hedges, R. E. M. (1995) · Journal of Archaeological Science · doi:10.1006/jasc.1995.0031 · Cited by 159
Neandertal Evolutionary Genetics: Mitochondrial DNA Data from the Iberian Peninsula
Lalueza‐Fox, C. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi094 · Cited by 158
Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers
Sánchez-Quinto, F., Schroeder, H., Ramirez, O., Ávila-Arcos, M. C., Pybus, M., Olalde, I., Velazquez, A. M. V., Marcos, M. E. P., Encinas, J. M. V., Bertranpetit, J., et al. (2012) · Current Biology · doi:10.1016/j.cub.2012.06.005 · Cited by 142
Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence
Orlando, L., Darlu, P., Toussaint, M., Bonjean, D., Otte, M., & Hänni, C. (2006) · Current Biology · doi:10.1016/j.cub.2006.05.019 · Cited by 136
Tracking down Human Contamination in Ancient Human Teeth
Sampietro, M. L., Gilbert, M. T. P., Lao, Ó., Caramelli, D., Lari, M., Bertranpetit, J., & Lalueza‐Fox, C. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl047 · Cited by 121
Dalén, L., Orlando, L., Shapiro, B., Durling, M. B., Quam, R., Gilbert, M. T. P., Fernández-Lomana, J. C. D., Willerslev, E., Arsuaga, J. L., & Götherström, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss074 · Cited by 96
A highly divergent mtDNA sequence in a Neandertal individual from Italy
Caramelli, D., Lalueza‐Fox, C., Condémi, S., Longo, L., Milani, L., Manfredini, A., Pierre, M. D. S., Adoni, F., Lari, M., Giunti, P., et al. (2006) · Current Biology · doi:10.1016/j.cub.2006.07.043 · Cited by 95
Lalueza‐Fox, C., Krause, J., Caramelli, D., Catalano, G., Milani, L., Sampietro, M. L., Calafell, F., Martı́nez-Maza, C., Bastir, M., García‐Tabernero, A., et al. (2006) · Current Biology · doi:10.1016/j.cub.2006.07.044 · Cited by 92
Surakka, I. L., Kristiansson, K., Anttila, Inouye, M., Barnes, C. P., Moutsianas, L., Salomaa, V. V., Daly, M. J., Palotie, A. V., Peltonen, L., et al. (2010) · Genome Research · doi:10.1101/gr.106534.110 · Cited by 53
Garcia‐Garcerà, M., Gigli, E., Sánchez‐Quinto, F., Ramírez, Ó., Calafell, F., Civit, S., & Lalueza‐Fox, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024161 · Cited by 50
Identifying conservation units within captive chimpanzee populations
Deinard, A. S., & Kídd, K. K. (2000) · American Journal of Physical Anthropology · doi:10.1002/(sici)1096-8644(200001)111:1 · Cited by 41
A Statistical Approach to Identify Ancient Template DNA
Helgason, A., Pálsson, S., Lalueza‐Fox, C., Ghosh, S., Sigurdardottir, S. L., Baker, A., Hrafnkelsson, B., Árnadóttir, L., Þorsteinsdóttir, U., & Stefánsson, K. (2007) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0259-8 · Cited by 29
Cited by
Sorted by citations
An early modern human from Romania with a recent Neanderthal ancestor
Fu, Q., Hajdinjak, M., Moldovan, O. T., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., et al. (2015) · Nature · doi:10.1038/nature14558 · Cited by 802
Self-citationThe genomic history of southeastern Europe
Mathieson, I., Alpaslan-Roodenberg, S., Posth, C., Szécsényi‐Nagy, A., Rohland, N., Mallick, S., Olalde, Í., Broomandkhoshbacht, N., Candilio, F., Cheronet, O., et al. (2018) · Nature · doi:10.1038/nature25778 · Cited by 759
Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
Meyer, M., Arsuaga, J.-L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., et al. (2016) · Nature · doi:10.1038/nature17405 · Cited by 584
Self-citationPartial uracil–DNA–glycosylase treatment for screening of ancient DNA
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S., & Reich, D. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0624 · Cited by 572
Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
Renaud, G., Slon, V., Duggan, A. T., & Kelso, J. (2015) · Genome Biology · doi:10.1186/s13059-015-0776-0 · Cited by 509
Metadata
- Authors
- Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., & Jakobsson, M.
- Affiliations
- Uppsala University (SE)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Russian Academy of Sciences (RU)
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences Siberian Branch, Novosibirsk 630090, Russia; and
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-01-27
- Volume
- 111
- Issue
- 6
- Pages
- 2229-2234
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3926038
- OpenAlex
- W2112954194
- Cited by
- 499
- References
- 58
- Citations by year
- 2026: 45 · 2025: 68 · 2024: 50 · 2023: 44 · 2022: 35 · 2021: 52 · 2020: 49 · 2019: 27 · 2018: 36 · 2017: 29 · 2016: 24 · 2015: 22 · 2014: 18
- FWCI
- 20.31
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- ancient DNA, Neanderthals, contamination control, mitochondrial genome, Siberia
- MeSH terms
- Animals, DNA, Mitochondrial, Humans, Molecular Sequence Data, Siberia, Neanderthals
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
