Patterns of damage in genomic DNA sequences from a neandertal
Open accessAbstract
High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.
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
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 authenticity of the human reads obtained from archaeological dental calculus and dentine was assessed by examining damage patterns typical of ancient DNA.
“The authenticity of the human reads obtained from archaeological dental calculus and dentine was assessed by examining damage patterns typical of ancient DNA (Briggs et al., 2007; Ginolhac et al., 2011; Jonsson et al., 2013).”
From Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus (2016) · cites this paper as Briggs et al., 2007
The Abstract and Results and Discussion describe characteristic ancient-DNA damage patterns, supporting their use as patterns to examine in the citing study. But Results and Discussion cautions that contaminating modern human DNA can show typical misincorporations, so damage patterns alone cannot reliably establish the authenticity of human reads. (LLM, conf=0.86)
Experimental — accuracy not yet measuredaDNA damage results in C-to-T and G-to-A substitutions.
“This therefore results in a pattern of C-to-T substitutions. When a double-stranded library preparation is used, these substitutions can occur on the opposite strand thus resulting in G-to-A substitutions due to base complementarity.”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [4]
An excess of C-to-T substitutions arise near read termini due to the accumulation of post-mortem cytosine deamination.
“An excess of these substitutions arise near read termini due to the accumulation of post-mortem cytosine deamination (Briggs et al. 2007).”
From Unravelling reference bias in ancient DNA datasets (2024) · cites this paper as Briggs et al. 2007
All samples showed nucleotide misincorporation patterns characteristic of ancient DNA.
“MapDamage 2.0 (ref. 60) has been used to evaluate fragment lengths and nucleotide misincorporation patterns of the provided samples, all of which showed levels that are characteristic for ancient DNA13.”
From Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods (2017) · cites this paper as [13]
Authentic ancient DNA exhibits characteristic damage including short DNA fragment lengths, a high rate of cytosine deamination at the termini of DNA fragments, and an enrichment of purine bases at DNA breakage sites.
“Briefly, authentic ancient DNA is known to exhibit characteristic damage that includes short DNA fragment lengths, a high rate of cytosine deamination at the termini of DNA fragments, and an enrichment of purine bases at DNA breakage sites.”
From Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus (2016) · cites this paper as Briggs et al., 2007
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works
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 · see citing works
Self-citationInstability and decay of the primary structure of DNA
Lindahl, T. (1993) · Nature · doi:10.1038/362709a0 · Cited by 5,679 · see citing works
Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison
Sankoff, D., & Kruskal, J. B. (1983) · Medical Entomology and Zoology · Cited by 1,940 · see citing works
Genetic analyses from ancient DNA
Pääbo, S., Poinar, H., Serre, D., Jaenicke-Després, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L., & Hofreiter, M. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.37.110801.143214 · Cited by 1,333 · see citing works
Self-citationNeandertal DNA sequences and the origin of modern humans.
Krings, M., Stone, A., Schmitz, R., Krainitzki, H., Stoneking, M., & Pääbo, S. (1997) · Cell · doi:10.1016/s0092-8674(00)80310-4 · Cited by 1,274 · see citing works
Self-citationAncient 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 1,011 · see citing works
Self-citationBentley, D. (2006) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2006.10.009 · Cited by 805 · see citing works
Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M., & Pääbo, S. (2001) · Nature Reviews Genetics · doi:10.1038/35072071 · Cited by 781 · see citing works
Self-citationAnalysis 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 · see citing works
Self-citationHofreiter, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4793 · Cited by 684 · see citing works
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 · see citing works
Self-citationMetagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
Poinar, H. N., Schwarz, C., Qi, J., Shapiro, B., MacPhee, R. D. E., Buigues, B., Tikhonov, A., Huson, D. H., Tomsho, L. P., Auch, A. F., et al. (2005) · Science · doi:10.1126/science.1123360 · Cited by 618 · see citing works
Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid
Lindahl, T. L., & Andersson, A. K. (1972) · Biochemistry · doi:10.1021/bi00769a019 · Cited by 592 · see citing works
Molecular 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 · see citing works
No Evidence of Neandertal mtDNA Contribution to Early Modern Humans
Serre, D., Langaney, A., Chech, M., Teschler‐Nicola, M., Paunović, M., Mennecier, P., Hofreiter, M., Possnert, G., & Pääbo, S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020057 · Cited by 437 · see citing works
Self-citationMoriya, M. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.3.1122 · Cited by 418 · see citing works
DNA Damage and DNA Sequence Retrieval from Ancient Tissues
Höss, M., Jaruga, P., Zastawny, T. H., Dizdaroğlu, M., & Pääbo, S. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.7.1304 · Cited by 403 · see citing works
Self-citationA 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 · see citing works
Self-citationBrotherton, 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 255 · see citing works
Mutagenesis and carcinogenesis caused by the oxidation of nucleic acids
Nakabeppu, Y., Sakumi, K., Sakamoto, K., Tsuchimoto, D., Tsuzuki, T., & Nakatsu, Y. (2006) · Biological Chemistry · doi:10.1515/bc.2006.050 · Cited by 255 · see citing works
Genomic Sequencing of Pleistocene Cave Bears
Noonan, J. P., Hofreiter, M., Smith, D. R., Priest, J. R., Rohland, N., Rabeder, G., Krause, J., Detter, J. C., Pääbo, S., & Rubin, E. M. (2005) · Science · doi:10.1126/science.1113485 · Cited by 242 · see citing works
Self-citationSchmitz, R. W., Serre, D., Bonani, G., Feine, S. C., Hillgruber, F., Krainitzki, H., Pääbo, S., & Smith, F. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.192464099 · Cited by 221 · see citing works
Self-citationStiller, M., Green, R. E., Ronan, M., Simons, J. F., Du, L., He, W., Egholm, M., Rothberg, J. M., Keates, S. G., Ovodov, N. D., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605327103 · Cited by 203 · see citing works
Self-citationRecharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis
Gilbert, M. T. P., Binladen, J., Miller, W., Wiuf, C., Willerslev, E., Poinar, H. N., Carlson, J. E., Leebens‐Mack, J., & Schuster, S. C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl483 · Cited by 200 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
A late Neandertal femur from Les Rochers-de-Villeneuve, France
Beauval, C., Maureille, B., Lacrampe‐Cuyaubère, F., Serre, D., Peressinotto, D., Bordes, J., Cochard, D., Couchoud, I., Dubrasquet, D., Laroulandie, V., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502656102 · Cited by 109 · see citing works
Self-citationA 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 · see citing works
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 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
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 · see citing works
Self-citationThe complete genome sequence of a Neanderthal from the Altai Mountains
Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature12886 · Cited by 2,254 · see citing works
Self-citationGenetic 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 · see citing works
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 · see citing works
Self-citationMassive migration from the steppe was a source for Indo-European languages in Europe
Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940 · see citing works
Self-citationmapDamage2.0: 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 · see citing works
Self-citationPopulation genomics of Bronze Age Eurasia
Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., et al. (2015) · Nature · doi:10.1038/nature14507 · Cited by 1,550 · see citing works
Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314445110 · Cited by 1,443 · see citing works
Self-citationRecalibrating equus evolution using the genome sequence of an early middle pleistocene horse
Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., et al. (2013) · Nature · doi:10.1038/nature12323 · Cited by 841 · see citing works
Self-citationAn 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 · see citing works
Self-citationA Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
Fu, Q., Mittnik, A., Johnson, P. L. F., Bos, K., Lari, M., Bollongino, R., Sun, C., Giemsch, L., Schmitz, R., Burger, J., et al. (2013) · Current Biology · doi:10.1016/j.cub.2013.02.044 · Cited by 709 · see citing works
Self-citationThe half-life of DNA in bone: measuring decay kinetics in 158 dated fossils
Allentoft, M. E., Collins, M., Harker, D., Haile, J., Oskam, C. L., Hale, M. L., Campos, P. F., Samaniego, J. A., Gilbert, M. T. P., Willerslev, E., et al. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.1745 · Cited by 633 · see citing works
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 · see citing works
Self-citationNuclear 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 · see citing works
Self-citationThe genome of a Late Pleistocene human from a Clovis burial site in western Montana
Rasmussen, M., Anzick, S. L., Waters, M. R., Skoglund, P., DeGiorgio, M., Stafford, T. W., Rasmussen, S., Moltke, I., Albrechtsen, A., Doyle, S. M., et al. (2014) · Nature · doi:10.1038/nature13025 · Cited by 562 · see citing works
Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Ávila-Arcos, M. C., Malaspinas, A.-S., et al. (2015) · Science · doi:10.1126/science.aab3884 · Cited by 540 · see citing works
Partial 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 · see citing works
A mitochondrial genome sequence of a hominin from Sima de los Huesos
Meyer, M., Fu, Q., Aximu-Petri, A., Glocke, I., Nickel, B., Arsuaga, J.-L., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., et al. (2014) · Nature · doi:10.1038/nature12788 · Cited by 534 · see citing works
Self-citationThe prehistoric peopling of Southeast Asia
McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J. V., van Driem, G., Gram Wilken, U., Seguin-Orlando, A., de la Fuente Castro, C., et al. (2018) · Science · doi:10.1126/science.aat3628 · Cited by 517 · see citing works
Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Vicente, M., Steyn, M., Soodyall, H., et al. (2017) · Science · doi:10.1126/science.aao6266 · Cited by 519 · see citing works
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 · see citing works
Self-citationSeparating endogenous ancient DNA from modern day contamination in a Siberian Neandertal
Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., & Jakobsson, M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318934111 · Cited by 499 · see citing works
Optimal ancient DNA yields from the inner ear part of the human petrous bone
Pinhasi, R., Fernandes, D., Sirak, K., Novak, M., Connell, S., Alpaslan-Roodenberg, S., Gerritsen, F., Moiseyev, V., Gromov, A., Raczky, P., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129102 · Cited by 487 · see citing works
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 · see citing works
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 · see citing works
Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411 · see citing works
Self-citationUpper Palaeolithic genomes reveal deep roots of modern Eurasians
Jones, E. R., Gonzalez-Fortes, G., Connell, S., Siska, V., Eriksson, A., Martiniano, R., McLaughlin, R. L., Gallego Llorente, M., Cassidy, L. M., Gamba, C., et al. (2015) · Nature Communications · doi:10.1038/ncomms9912 · Cited by 417 · see citing works
Estimating genetic kin relationships in prehistoric populations
Monroy Kuhn, J. M., Jakobsson, M., & Günther, T. (2018) · PLOS ONE · doi:10.1371/journal.pone.0195491 · Cited by 330 · see citing works
mapDamage: testing for damage patterns in ancient DNA sequences
Ginolhac, A., Rasmussen, M., Gilbert, M. T. P., Willerslev, E., & Orlando, L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr347 · Cited by 363 · see citing works
Improving ancient DNA read mapping against modern reference genomes
Schubert, M., Ginolhac, A., Lindgreen, S., Thompson, J. F., AL-Rasheid, K. A., Willerslev, E., Krogh, A., & Orlando, L. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-178 · Cited by 325 · see citing works
Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416991111 · Cited by 324 · see citing works
Dabney, J., & Meyer, M. (2012) · BioTechniques · doi:10.2144/000113809 · Cited by 316 · see citing works
Self-citationGenomic structure in Europeans dating back at least 36,200 years
Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., et al. (2014) · Science · doi:10.1126/science.aaa0114 · Cited by 315 · see citing works
Archaeogenomic evidence reveals prehistoric matrilineal dynasty
Kennett, D. J., Plog, S., George, R. J., Culleton, B. J., Watson, A. S., Skoglund, P., Rohland, N., Mallick, S., Stewardson, K., Kistler, L., et al. (2017) · Nature Communications · doi:10.1038/ncomms14115 · Cited by 301 · see citing works
Günther, T., & Nettelblad, C. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008302 · Cited by 228 · see citing works
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 · see citing works
Schuenemann, V. J., Peltzer, A., Welte, B., van Pelt, W. P., Molak, M., Wang, C.-C., Furtwängler, A., Urban, C., Reiter, E., Nieselt, K., et al. (2017) · Nature Communications · doi:10.1038/ncomms15694 · Cited by 201 · see citing works
Self-citationThe 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 · see citing works
Self-citationChain and conformation stability of solid-state DNA: implications for room temperature storage
Bonnet, J., Colotte, M., Coudy, D., Couallier, V., Portier, J., Morin, B., & Tuffet, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1060 · Cited by 182 · see citing works
Computational challenges in the analysis of ancient DNA
Prüfer, K., Stenzel, U., Hofreiter, M., Pääbo, S., Kelso, J., & Green, R. E. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r47 · Cited by 155 · see citing works
“These changes cluster primarily at the 3' and 5' end of the molecules, probably due to single-stranded overhangs that are more susceptible to deamination at the end of the sequenced molecules [19].”
BackgroundMethodInfluentialSelf-citationAncient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity
Yang, M. A., Malaspinas, A.-S., Durand, E. Y., & Slatkin, M. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss117 · Cited by 101 · see citing works
Joint estimates of heterozygosity and runs of homozygosity for modern and ancient samples
Renaud, G., Hanghøj, K., Korneliussen, T. S., Willerslev, E., & Orlando, L. (2019) · Genetics · doi:10.1534/genetics.119.302057 · Cited by 101 · see citing works
Human evolution: a tale from ancient genomes
Llamas, B., Willerslev, E., & Orlando, L. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0484 · Cited by 100 · see citing works
Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
Peyrégne, S., Slon, V., Mafessoni, F., de Filippo, C., Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Le Cabec, A., Wehrberger, K., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw5873 · Cited by 82 · see citing works
Self-citationSuccessful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus
Ozga, A. T., Nieves‐Colón, M. A., Honap, T. P., Sankaranarayanan, K., Hofman, C. A., Milner, G. R., Lewis, C. M., Stone, A. C., & Warinner, C. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22960 · Cited by 79 · see citing works
“The authenticity of the human reads obtained from archaeological dental calculus and dentine was assessed by examining damage patterns typical of ancient DNA (Briggs et al., 2007; Ginolhac et al., 2011; Jonsson et al., 2013).”
snpAD: an ancient DNA genotype caller
Prüfer, K. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty507 · Cited by 78 · see citing works
Self-citationComplete mitochondrial DNA genome sequences from the first New Zealanders
Knapp, M., Horsburgh, K. A., Prost, S., Stanton, J.-A., Buckley, H. R., Walter, R. K., & Matisoo-Smith, E. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1209896109 · Cited by 61 · see citing works
Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences
de Filippo, C., Meyer, M., & Prüfer, K. (2018) · BMC Biology · doi:10.1186/s12915-018-0581-9 · Cited by 53 · see citing works
Self-citationGenetic Ancestry of Rapanui before and after European Contact
Fehren-Schmitz, L., Jarman, C. L., Harkins, K. M., Kayser, M., Popp, B. N., & Skoglund, P. (2017) · Current Biology · doi:10.1016/j.cub.2017.09.029 · Cited by 47 · see citing works
Malaspinas, A.-S., Tange, O., Moreno-Mayar, J. V., Rasmussen, M., DeGiorgio, M., Wang, Y., Valdiosera, C. E., Politis, G., Willerslev, E., & Nielsen, R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu410 · Cited by 45 · see citing works
Analysis of human accelerated DNA regions using archaic hominin genomes
Burbano, H. A., Green, R. E., Maricic, T., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Kelso, J., Pollard, K. S., Lachmann, M., & Pääbo, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032877 · Cited by 46 · see citing works
Self-citationUnravelling reference bias in ancient DNA datasets
Dolenz, S., van der Valk, T., Jin, C., Oppenheimer, J., Sharif, M. B., Orlando, L., Shapiro, B., Dalén, L., & Heintzman, P. D. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae436 · Cited by 33 · see citing works
“An excess of these substitutions arise near read termini due to the accumulation of post-mortem cytosine deamination (Briggs et al. 2007).”
BackgroundLopez-Valenzuela, M., Ramirez, O., Rosas, A., Garcia-Vargas, S., de la Rasilla, M., Lalueza-Fox, C., & Espinosa-Parrilla, Y. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss023 · Cited by 31 · see citing works
The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals
Peyrégne, S., Kelso, J., Peter, B. M., & Pääbo, S. (2022) · eLife · doi:10.7554/elife.75464 · Cited by 24 · see citing works
Self-citationMoreno-Mayar, J. V., Korneliussen, T. S., Dalal, J., Renaud, G., Albrechtsen, A., Nielsen, R., & Malaspinas, A.-S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz660 · Cited by 21 · see citing works
Maternal Genetic History of Southern East Asians over the Past 12,000 Years
Liu, Y., Wang, T., Wu, X., Fan, X., Wang, W., Xie, G., Li, Z., Yang, Q., Cao, P., Yang, R., et al. (2021) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2021.06.002 · Cited by 21 · see citing works
Xu, W., Lin, Y., Zhao, K., Li, H., Tian, Y., Ngatia, J. N., Ma, Y., Sahu, S. K., Guo, H., Guo, X., et al. (2021) · Ecology and Evolution · doi:10.1002/ece3.7056 · Cited by 20 · see citing works
Moreno-Mayar, J. V. (2022) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkab357 · Cited by 4 · see citing works
<tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings
Rubin, J., van Waaij, J., Kraft, L., Sirén, J., Sackett, P. W., & Renaud, G. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf170 · Cited by 1 · see citing works
“The most characteristic hallmark of aDNA, however, re-sults from the hydrolytic cleavage of amino groups from certain nucleobases resulting from long-term exposure to moisture and is known as deamination [ 1 , 4 , 5 ].”
- Authors
- 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., & Pääbo, S.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- University of California, Berkeley (US)
- 454 Life Sciences, Branford, CT 06405
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2007-09-11
- Volume
- 104
- Issue
- 37
- Pages
- 14616-14621
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1976210
- OpenAlex
- W2156330112
- Cited by
- 981
- References
- 32
- Citations by year
- 2026: 57 · 2025: 67 · 2024: 67 · 2023: 51 · 2022: 59 · 2021: 85 · 2020: 83 · 2019: 62 · 2018: 76 · 2017: 69 · 2016: 52 · 2015: 51 · 2014: 44 · 2013: 39 · 2012: 33
- FWCI
- 108.87
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Max-Planck-Gesellschaft
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM040282, R01‑GM40282)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Neanderthals, ancient DNA, DNA damage, depurination, cytosine deamination, substitution patterns, DNA strand breaks, Nick, mammoth, cave bear, DNA degradation
- MeSH terms
- Base Sequence, Computer Simulation, Cytosine, Deamination, DNA, DNA Damage, DNA-Directed DNA Polymerase, Humans, Models, Biological, Molecular Sequence Data, Paleontology, Reference Standards, Templates, Genetic, Genomic Library, Likelihood Functions, Polymerase Chain Reaction, Genome, Bacteriophage T4, Sequence Analysis, DNA, History, Ancient
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
