Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
Open accessAbstract
UNLABELLED: Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates. AVAILABILITY: https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.
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 study provides the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods and assessing authenticity via nucleotide misincorporation patterns and statistical contamination tests.
“Here, we provide the first reliable data set obtained from ancient Egyptians using high-throughput DNA sequencing methods and assessing the authenticity of the retrieved ancient DNA via characteristic nucleotide misincorporation patterns1314 and statistical contamination tests15 to ensure the ancient origin of our obtained data.”
From Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods (2017) · cites this paper as [15]
Human mitochondrial DNA contamination was measured using schmutzi.
“(iii) We measured human mitochondrial DNA contamination using schmutzi (40).”
From Ancient DNA sheds light on the genetic origins of early Iron Age Philistines (2019) · cites this paper as [40]
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
ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982 · see citing works
The 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-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-citationUpdated comprehensive phylogenetic tree of global human mitochondrial DNA variation
van Oven, M., & Kayser, M. (2009) · Human Mutation · doi:10.1002/humu.20921 · Cited by 1,810 · see citing works
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 · see citing works
Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
Self-citationGenome sequence of a 45,000-year-old modern human from western Siberia
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023 · see citing works
Self-citationPatterns 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 · see citing works
Self-citationThe 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 792 · see citing works
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 · see citing works
A 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
Metagenomics 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
A 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 601 · see citing works
Self-citationSequence-specific error profile of Illumina sequencers
Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M. C., Hirai, A. M., Takahashi, H., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr344 · Cited by 593 · 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
Kloss‐Brandstätter, A., Pacher, D., Schönherr, S., Weißensteiner, H., Binna, R., Specht, G., & Kronenberg, F. (2010) · Human Mutation · doi:10.1002/humu.21382 · Cited by 503 · see citing works
Separating 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
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
Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
Olalde, I., Allentoft, M. E., Sánchez-Quinto, F., Santpere, G., Chiang, C. W. K., DeGiorgio, M., Prado-Martinez, J., Rodríguez, J. A., Rasmussen, S., Quilez, J., et al. (2014) · Nature · doi:10.1038/nature12960 · Cited by 360 · see citing works
SHRiMP2: Sensitive yet Practical Short Read Mapping
David, M., Dzamba, M., Lister, D., Ilie, L., & Brudno, M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr046 · Cited by 348 · see citing works
leeHom: adaptor trimming and merging for Illumina sequencing reads
Renaud, G., Stenzel, U., & Kelso, J. F. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku699 · Cited by 274 · 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
Inconsistencies in Neanderthal Genomic DNA Sequences
Wall, J. D., & Kim, S. K. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030175 · Cited by 180 · 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 · cited 2× · see citing works
“After the death of an organism, the endogenous DNA begins to degrade and accumulates chemical damage. aDNA molecules, therefore, tend to be quite short, typically less than 60 bases in length [1], and carry uracils as a result of cytosine deam-ination.”
BackgroundInfluentialSelf-citationSelective enrichment of damaged DNA molecules for ancient genome sequencingPreprint
Gansauge, M.-T., & Meyer, M. (2014) · Genome Research · doi:10.1101/gr.174201.114 · Cited by 114 · see citing works
Migration and Interaction in a Contact Zone: mtDNA Variation among Bantu-Speakers in Southern Africa
Barbieri, C., Vicente, M., Oliveira, S., Bostoen, K. A. G., Rocha, J., Stoneking, M., & Pakendorf, B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099117 · Cited by 99 · see citing works
Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity
Bandelt, H. (2005) · European Journal of Human Genetics · doi:10.1038/sj.ejhg.5201476 · Cited by 53 · see citing works
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 · see citing works
Duggan, A. T., Whitten, M., Wiebe, V., Crawford, M., Butthof, A., Va, S., Makarov, S., Novgorodov, I. N., Осаковский, В. Л., & Pakendorf, B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083570 · Cited by 49 · see citing works
Self-citationImpacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study
Parks, M., & Lambert, D. M. (2015) · BMC Genomics · doi:10.1186/s12864-015-1219-8 · Cited by 32 · see citing works
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 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
EAGER: efficient ancient genome reconstruction
Peltzer, A., Jäger, G., Herbig, A., Seitz, A., Kniep, C., Krause, J., & Nieselt, K. (2016) · Genome Biology · doi:10.1186/s13059-016-0918-z · Cited by 509 · see citing works
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works
The population history of northeastern Siberia since the Pleistocene
Sikora, M., Питулько, В. В., Sousa, V. C., Allentoft, M. E., Vinner, L., Rasmussen, S., Margaryan, A., Damgaard, P. D. B., Castro, C. D. L. F., Renaud, G., et al. (2019) · Nature · doi:10.1038/s41586-019-1279-z · Cited by 433 · see citing works
Self-citationReconstructing Prehistoric African Population Structure
Skoglund, P., Thompson, J. C., Prendergast, M. E., Mittnik, A., Sirak, K. A., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Peltzer, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.08.049 · Cited by 410 · 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
Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration
Gerber, T., Murawala, P., Knapp, D., Masselink, W., Schuez, M., Hermann, S., Gac-Santel, M., Nowoshilow, S., Kageyama, J., Khattak, S., et al. (2018) · Science · doi:10.1126/science.aaq0681 · Cited by 415 · see citing works
Posth, C., Renaud, G., Mittnik, A., Drucker, D. G., Rougier, H., Cupillard, C., Valentin, F., Thevenet, C., Furtwängler, A., Wißing, C., et al. (2016) · Current Biology · doi:10.1016/j.cub.2016.01.037 · Cited by 401 · see citing works
Self-citationReconstructing the Deep Population History of Central and South America
Posth, C., Nakatsuka, N. J., Lazaridis, I., Skoglund, P., Mallick, S., Lamnidis, T. C., Rohland, N., Nägele, K., Adamski, N., Bertolini, E., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.027 · Cited by 391 · see citing works
Early human dispersals within the Americas
Moreno-Mayar, J. V., Vinner, L., Damgaard, P. D. B., Castro, C. D. L. F., Chan, J., Spence, J. P., Allentoft, M. E., Vimala, T., Racimo, F., Pinotti, T., et al. (2018) · Science · doi:10.1126/science.aav2621 · Cited by 365 · see citing works
Ancient genomes from northern China suggest links between subsistence changes and human migration
Ning, C., Li, T., Wang, K., Zhang, F., Li, T., Wu, X., Gao, S., Zhang, Q., Hai, Z., Hudson, M. J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16557-2 · Cited by 343 · see citing works
Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers
Sikora, M., Seguin‐Orlando, A., Sousa, V. C., Albrechtsen, A., Korneliussen, T. S., Ko, A., Rasmussen, S., Dupanloup, I., Nigst, P. R., Bosch, M. D., et al. (2017) · Science · doi:10.1126/science.aao1807 · Cited by 333 · see citing works
Self-citationPopulation genomics of the Viking world
Margaryan, A., Lawson, D. J., Sikora, M., Racimo, F., Rasmussen, S., Moltke, I., Cassidy, L. M., Jørsboe, E., Ingason, A., Pedersen, M. W., et al. (2020) · Nature · doi:10.1038/s41586-020-2688-8 · Cited by 336 · see citing works
Self-citationEstimating 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
Posth, C., Wißing, C., Kitagawa, K., Pagani, L., van Holstein, L. A., Racimo, F., Wehrberger, K., Conard, N. J., Kind, C.-J., Bocherens, H., et al. (2017) · Nature Communications · doi:10.1038/ncomms16046 · Cited by 311 · see citing works
Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria
Hublin, J., Sirakov, N., Aldeias, V., Bailey, S. E., Bard, É., Delvigne, V., Endarova, E., Fagault, Y., Fewlass, H., Hajdinjak, M., et al. (2020) · Nature · doi:10.1038/s41586-020-2259-z · Cited by 313 · see citing works
A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe
Jeong, C., Wang, K., Wilkin, S., Taylor, W. T. T., Miller, B. K., Bemmann, J., Stahl, R., Chiovelli, C., Knolle, F., Ulziibayar, S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.015 · Cited by 313 · see citing works
Ancient Rome: A genetic crossroads of Europe and the Mediterranean
Antonio, M. L., Gao, Z., Moots, H. M., Lucci, M., Candilio, F., Sawyer, S., Oberreiter, V., Calderon, D., Devitofranceschi, K., Aikens, R. C., et al. (2019) · Science · doi:10.1126/science.aay6826 · Cited by 294 · see citing works
Kinship-based social inequality in Bronze Age Europe
Mittnik, A., Massy, K., Knipper, C., Wittenborn, F., Friedrich, R., Pfrengle, S., Burri, M., Carlichi-Witjes, N., Deeg, H., Furtwängler, A., et al. (2019) · Science · doi:10.1126/science.aax6219 · Cited by 300 · see citing works
The genetic prehistory of the Baltic Sea region
Mittnik, A., Wang, C., Pfrengle, S., Daubaras, M., Zariņa, G., Hallgren, F., Allmäe, R., Khartanovich, V. I., Moiseyev, V. G., Tõrv, M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-02825-9 · Cited by 322 · see citing works
A guide to ancient protein studies
Hendy, J., Welker, F., Demarchi, B., Speller, C., Warinner, C., & Collins, M. J. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0510-x · Cited by 291 · see citing works
Genetic origins of the Minoans and Mycenaeans
Lazaridis, I., Mittnik, A., Patterson, N. J., Mallick, S., Rohland, N., Pfrengle, S., Furtwängler, A., Peltzer, A., Posth, C., Vasilakis, A., et al. (2017) · Nature · doi:10.1038/nature23310 · Cited by 275 · see citing works
Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers
Posth, C., He, Y. H., Ghalichi, A., Rougier, H., Crèvecoeur, I., Huang, Y., Ringbauer, H., Rohrlach, A. B., Nägele, K., Villalba‐Mouco, V., et al. (2023) · Nature · doi:10.1038/s41586-023-05726-0 · Cited by 275 · see citing works
Slatkin, M., & Racimo, F. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1524306113 · Cited by 252 · see citing works
The genetic history of admixture across inner Eurasia
Jeong, C., Balanovsky, O. P., Lukianova, E., Kahbatkyzy, N., Flegontov, P., Владимирович, З. В., Immel, A., Wang, C., Iksan, O., Khussainova, E., et al. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0878-2 · Cited by 245 · see citing works
Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations
van de Loosdrecht, M. S., Bouzouggar, A., Humphrey, L., Posth, C., Barton, N., Aximu‐Petri, A., Nickel, B., Nagel, S., Talbi, E. H., Hajraoui, M. A. E., et al. (2018) · Science · doi:10.1126/science.aar8380 · Cited by 241 · see citing works
Language continuity despite population replacement in Remote Oceania
Posth, C., Nägele, K., Colleran, H., Valentin, F., Bedford, S., Kami, K. W., Shing, R., Buckley, H., Kinaston, R., Walworth, M., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0498-2 · Cited by 233 · see citing works
Llamas, B., Valverde, G., Fehren‐Schmitz, L., Weyrich, L. S., Cooper, A., & Haak, W. (2016) · STAR Science & Technology of Archaeological Research · doi:10.1080/20548923.2016.1258824 · Cited by 217 · see citing works
Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia
He, Y. H., Spyrou, M. A., Karapetian, M. K., Shnaider, S. V., Radzevičiūtė, R., Nägele, K., Neumann, G. U., Penske, S., Zech, J., Lucas, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.037 · Cited by 218 · see citing works
Population genomics of post-glacial western Eurasia
Allentoft, M. E., Sikora, M., Refoyo-Martínez, A., Irving-Pease, E. K., Fischer, A., Barrie, W., Ingason, A., Stenderup, J. T., Sjögren, K.-G., Pearson, A., et al. (2024) · Nature · doi:10.1038/s41586-023-06865-0 · Cited by 263 · see citing works
Self-citationTriangulation supports agricultural spread of the Transeurasian languages
Robbeets, M., Bouckaert, R., Conte, M., Savelyev, A., Li, T., An, D.-I., Shinoda, K., Cui, Y., Kawashima, T., Kim, G., et al. (2021) · Nature · doi:10.1038/s41586-021-04108-8 · Cited by 210 · see citing works
Knipper, C., Mittnik, A., Massy, K., Kociumaka, C., Küçükkalıpçı, İ., Maus, M., Wittenborn, F., Metz, S. E., Staskiewicz, A., Krause, J., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706355114 · Cited by 211 · 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
Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe
Jeong, C., Wilkin, S., Amgalantugs, T., Bouwman, A., Taylor, W. T. T., Hagan, R. W., Bromage, S., Tsolmon, S., Trachsel, C., Grossmann, J., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1813608115 · Cited by 199 · see citing works
The genomic origins of the Bronze Age Tarim Basin mummies
Zhang, F., Ning, C., Scott, A., Fu, Q., Bjørn, R., Li, W., Wei, D., Wang, W., Fan, L., Abuduresule, I., et al. (2021) · Nature · doi:10.1038/s41586-021-04052-7 · Cited by 193 · see citing works
Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave
Schroeder, H., Margaryan, A., Szmyt, M., Theulot, B., Włodarczak, P., Rasmussen, S., Gopalakrishnan, S., Szczepanek, A., Konopka, T., Jensen, T. Z. T., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1820210116 · Cited by 195 · see citing works
A Paleogenomic Reconstruction of the Deep Population History of the Andes
Nakatsuka, N. J., Lazaridis, I., Barbieri, C., Skoglund, P., Rohland, N., Mallick, S., Posth, C., Harkins, K. M., Ferry, M., Harney, É., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.015 · Cited by 190 · see citing works
Multiple migrations to the Philippines during the last 50,000 years
Larena, M., Sánchez‐Quinto, F., Sjödin, P., McKenna, J., Ebeo, C., Reyes, R., Casel, O., Huang, J., Hagada, K. P., Guilay, D., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2026132118 · Cited by 187 · see citing works
The Anglo-Saxon migration and the formation of the early English gene pool
Gretzinger, J., Sayer, D., Justeau, P., Altena, E., Pala, M., Dulias, K., Edwards, C. J., Jodoin, S., Lacher, L., Sabin, S. J., et al. (2022) · Nature · doi:10.1038/s41586-022-05247-2 · Cited by 176 · see citing works
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
Yates, J. A. F., Lamnidis, T. C., Borry, M., Valtueña, A. A., Fagernäs, Z., Clayton, S., Garcia, M. U., Neukamm, J., & Peltzer, A. (2021) · PeerJ · doi:10.7717/peerj.10947 · Cited by 13 · see citing works
The genetic prehistory of the Andean highlands 7000 years BP though European contact
Lindo, J., Haas, R., Hofman, C. A., Apata, M., Moraga, M. L., Verdugo, R. A., Watson, J. T., Llave, C. V., Witonsky, D., Pacheco, E. V., et al. (2018) · Science Advances · doi:10.1126/sciadv.aau4921 · Cited by 157 · see citing works
Dynamic changes in genomic and social structures in third millennium BCE central Europe
Papac, L., Ernée, M., Dobeš, M., Langová, M., Rohrlach, A. B., Aron, F., Neumann, G. U., Spyrou, M. A., Rohland, N., Velemínský, P., et al. (2021) · Science Advances · doi:10.1126/sciadv.abi6941 · Cited by 164 · see citing works
Lindo, J., Achilli, A., Perego, U. A., Archer, D., Valdiosera, C. E., Petzelt, B., Mitchell, J., Worl, R., Dixon, E. J., Fifield, T. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620410114 · Cited by 154 · see citing works
Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia
Marcus, J. H., Posth, C., Ringbauer, H., Lai, L., Skeates, R., Sidore, C., Beckett, J. F., Furtwängler, A., Olivieri, A., Chiang, C. W. K., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14523-6 · Cited by 164 · see citing works
Ancient DNA from Guam and the peopling of the Pacific
Pugach, I., Hübner, A., Hung, H., Meyer, M., Carson, M. T., & Stoneking, M. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2022112118 · Cited by 145 · see citing works
Emergence of human-adapted Salmonella enterica is linked to the Neolithization process
Key, F. M., Posth, C., Gomez, L. R. E., Hübler, R., Spyrou, M. A., Neumann, G. U., Furtwängler, A., Sabin, S. J., Burri, M., Wissgott, A., et al. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1106-9 · Cited by 145 · see citing works
Wang, K., Goldstein, S. T., Bleasdale, M., Clist, B., Bostoen, K. A. G., Bakwa-Lufu, P., Buck, L. T., Crowther, A., Dème, A., McIntosh, R. J., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz0183 · Cited by 143 · see citing works
Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus
Skourtanioti, E., Erdal, Y. S., Frangipane, M., Restelli, F. B., Yener, K. A., Pinnock, F., Matthiae, P., Özbal, R., Schoop, U.-D., Guliyev, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.044 · Cited by 140 · see citing works
Ning, C., Wang, C., Gao, S., Yang, Y., Zhang, X., Wu, X., Zhang, F., Nie, Z., Tang, Y., Robbeets, M., et al. (2019) · Current Biology · doi:10.1016/j.cub.2019.06.044 · Cited by 139 · see citing works
A 5700 year-old human genome and oral microbiome from chewed birch pitch
Jensen, T. Z. T., Niemann, J., Iversen, K., Fotakis, A. K., Gopalakrishnan, S., Vågene, Å. J., Pedersen, M. W., Sinding, M. S., Ellegaard, M. R., Allentoft, M. E., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13549-9 · Cited by 134 · see citing works
Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia
Feldman, M., Fernández‐Domínguez, E., Reynolds, L., Baird, D., Pearson, J. A., Hershkovitz, I., May, H., Goring‐Morris, A. N., Benz, M., Gresky, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09209-7 · Cited by 128 · see citing works
Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
Kanzawa‐Kiriyama, H., Jinam, T. A., Kawai, Y., Sato, T. K., Hosomichi, K., Tajima, A., Adachi, N., Matsumura, H., Kryukov, K. A., Saitou, N., et al. (2019) · Anthropological Science · doi:10.1537/ase.190415 · Cited by 126 · see citing works
The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect
Posth, C., Zaro, V., Spyrou, M. A., Vai, S., Gnecchi‐Ruscone, G. A., Modi, A., Peltzer, A., Mötsch, A., Nägele, K., Vågene, Å. J., et al. (2021) · Science Advances · doi:10.1126/sciadv.abi7673 · Cited by 127 · see citing works
The genetic origin of Huns, Avars, and conquering Hungarians
Maróti, Z., Neparáczki, E., Schütz, O., Maár, K., Varga, G. I. B., Kovács, B., Kalmár, T., Nyerki, E., Nagy, I., Latinovics, D., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.04.093 · Cited by 132 · see citing works
Ancient genomes from present-day France unveil 7,000 years of its demographic history
Brunel, S., Bennett, E. A., Cardin, L., Garraud, D., Barrand-Emam, H., Beylier, A., Boulestin, B., Chenal, F., Ciesielski, E., Convertini, F., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1918034117 · Cited by 117 · see citing works
Haber, M., Doumet-Serhal, C., Scheib, C., Xue, Y., Danecek, P., Mezzavilla, M., Youhanna, S., Martiniano, R., Prado-Martinez, J., Szpak, M., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.06.013 · Cited by 121 · see citing works
Ancient DNA sheds light on the genetic origins of early Iron Age Philistines
Feldman, M., Master, D. M., Bianco, R. A., Burri, M., Stockhammer, P. W., Mittnik, A., Aja, A. J., Jeong, C., & Krause, J. (2019) · Science Advances · doi:10.1126/sciadv.aax0061 · Cited by 120 · see citing works
Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication
Key, F. M., Posth, C., Krause, J., Herbig, A., & Bos, K. I. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.05.005 · Cited by 112 · see citing works
Genomic insights into the early peopling of the Caribbean
Nägele, K., Posth, C., Iraeta-Orbegozo, M., de Armas, Y. C., Godoy, S. T. H., Herrera, U. M. G., Nieves-Colón, M. A., Sandoval‐Velasco, M., Mylopotamitaki, D., Radzevičiūtė, R., et al. (2020) · Science · doi:10.1126/science.aba8697 · Cited by 116 · see citing works
Ancient genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites
Gnecchi‐Ruscone, G. A., Szécsényi‐Nagy, A., Koncz, I., Csiky, G., Rácz, Z., Rohrlach, A. B., Brandt, G., Rohland, N., Csáky, V., Cheronet, O., et al. (2022) · Cell · doi:10.1016/j.cell.2022.03.007 · Cited by 117 · see citing works
Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians
Gnecchi‐Ruscone, G. A., Khussainova, E., Kahbatkyzy, N., Musralina, L., Spyrou, M. A., Bianco, R. A., Radzevičiūtė, R., Martins, N. F. G., Freund, C., Iksan, O., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe4414 · Cited by 115 · see citing works
Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean
Skourtanioti, E., Ringbauer, H., Gnecchi‐Ruscone, G. A., Bianco, R. A., Burri, M., Freund, C., Furtwängler, A., Martins, N. F. G., Knolle, F., Neumann, G. U., et al. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01952-3 · Cited by 103 · see citing works
Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago
Siska, V., Jones, E. R., Jeon, S., Bhak, Y., Kim, H., Cho, Y. S., Kim, H., Kyusang, L., Veselovskaya, E. V., Balueva, T. S., et al. (2017) · Science Advances · doi:10.1126/sciadv.1601877 · Cited by 101 · see citing works
Fregel, R., Ordóñez, A. C., Santana, J., Cabrera, V. M., Vázquez, J. V., Barroso, V. A., Moreno-Benítez, M., Delgado‐Darias, T., Rodríguez, A. R., Hernández, J. C., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0209125 · Cited by 107 · see citing works
Genome of a middle Holocene hunter-gatherer from Wallacea
Carlhoff, S., Duli, A., Nägele, K., Nur, M., Skov, L., Sumantri, I., Oktaviana, A. A., Hakim, B., Burhan, B., Syahdar, F. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03823-6 · Cited by 104 · see citing works
Contamination detection in sequencing studies using the mitochondrial phylogenyPreprint
Weißensteiner, H., Forer, L., Fendt, L., Kheirkhah, A., Salas, A., Kronenberg, F., & Schönherr, S. (2021) · Genome Research · doi:10.1101/gr.256545.119 · Cited by 99 · see citing works
Population genomics of postglacial western eurasiaPreprint
Allentoft, M. E., Sikora, M., Refoyo-Martínez, A., Irving-Pease, E. K., Fischer, A., Barrie, W., Ingason, A., Stenderup, J. T., Sjögren, K.-G., Pearson, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.04.490594 · Cited by 103 · see citing works
Self-citationArchaeogenomic distinctiveness of the Isthmo-Colombian area
Capodiferro, M. R., Aram, B., Raveane, A., Migliore, N. R., Colombo, G., Ongaro, L., Sandoval, J., Mendizábal, T., Mora, I. H., Tribaldos, M., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.040 · Cited by 102 · 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
Ancient nuclear genomes enable repatriation of Indigenous human remains
Wright, J. L., Wasef, S., Heupink, T. H., Westaway, M., Rasmussen, S., Pardoe, C., Fourmile, G. G., Young, M., Johnson, T., Slade, J., et al. (2018) · Science Advances · doi:10.1126/sciadv.aau5064 · Cited by 97 · see citing works
Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations
Juras, A., Chyleński, M., Ehler, E., Malmström, H., Żurkiewicz, D., Włodarczak, P., Wilk, S., Peška, J., Fojtík, P., Králík, M., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-29914-5 · Cited by 96 · see citing works
Sabin, S. J., Herbig, A., Vågene, Å. J., Ahlström, T., Božović, G., Arcini, C., Kühnert, D., & Bos, K. I. (2020) · Genome biology · doi:10.1186/s13059-020-02112-1 · Cited by 92 · see citing works
Matsumura, H., Shinoda, K., Shimanjuntak, T., Oktaviana, A. A., Noerwidi, S., Sofian, H. O., Prastiningtyas, D., Nguyen, L. C., Kakuda, T., Kanzawa‐Kiriyama, H., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198689 · Cited by 93 · see citing works
Majander, K., Pfrengle, S., Kocher, A., Neukamm, J., du Plessis, L., Pla-Díaz, M., Arora, N., Akgül, G., Salo, K., Schats, R., et al. (2020) · Current Biology · doi:10.1016/j.cub.2020.07.058 · Cited by 87 · see citing works
A systematic investigation of human DNA preservation in medieval skeletons
Parker, C., Rohrlach, A. B., Friederich, S., Nagel, S., Meyer, M., Krause, J., Bos, K. I., & Haak, W. (2020) · Scientific Reports · doi:10.1038/s41598-020-75163-w · Cited by 88 · see citing works
Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains
Schuenemann, V. J., Lankapalli, A. K., Barquera, R., Nelson, E. A., Hernández-Zaragoza, D. I., Acuña-Alonzo, V., Bos, K. I., Morfín, L. M., Herbig, A., & Krause, J. (2018) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0006447 · Cited by 88 · see citing works
Stable population structure in Europe since the Iron Age, despite high mobility
Antonio, M. L., Weiß, C. L., Gao, Z., Sawyer, S., Oberreiter, V., Moots, H. M., Spence, J. P., Cheronet, O., Zagorc, B., Praxmarer, E., et al. (2023) · eLife · doi:10.7554/elife.79714 · Cited by 81 · see citing works
Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland
Furtwängler, A., Rohrlach, A. B., Lamnidis, T. C., Papac, L., Neumann, G. U., Siebke, I., Reiter, E., Steuri, N., Hald, J., Denaire, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15560-x · Cited by 80 · see citing works
Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment
Gelabert, P., Sawyer, S., Bergström, A., Margaryan, A., Collin, T. C., Meshveliani, T., Belfer‐Cohen, A., Lordkipanidze, D., Jakeli, N., Matskevich, Z., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.06.023 · Cited by 77 · see citing works
snpAD: an ancient DNA genotype caller
Prüfer, K. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty507 · Cited by 78 · see citing works
Le, T., Yuan, H., Zhu, K., Liu, X., Guo, J., Min, R., He, H., Cao, D., Yang, X., Zhou, Z., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.09.055 · Cited by 74 · see citing works
Network of large pedigrees reveals social practices of Avar communities
Gnecchi‐Ruscone, G. A., Rácz, Z., Samu, L., Szeniczey, T., Faragó, N., Knipper, C., Friedrich, R., Zlámalová, D., Traverso, L., Liccardo, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07312-4 · Cited by 72 · see citing works
The Recovery, Interpretation and Use of Ancient Pathogen Genomes
Duchêne, S., Ho, S. Y. W., Carmichael, A. G., Holmes, E. C., & Poinar, H. N. (2020) · Current Biology · doi:10.1016/j.cub.2020.08.081 · Cited by 66 · see citing works
Peyrégne, S., & Peter, B. M. (2020) · Genome biology · doi:10.1186/s13059-020-02123-y · Cited by 71 · see citing works
Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
Furtwängler, A., Reiter, E., Neumann, G. U., Siebke, I., Steuri, N., Hafner, A., Lösch, S., Anthes, N., Schuenemann, V. J., & Krause, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-32083-0 · Cited by 62 · see citing works
Origin and Health Status of First-Generation Africans from Early Colonial Mexico
Barquera, R., Lamnidis, T. C., Lankapalli, A. K., Kocher, A., Hernández-Zaragoza, D. I., Nelson, E. A., Zamora-Herrera, A. C., Pérez-Ramallo, P., Felipe, N. B., Immel, A., et al. (2020) · Current Biology · doi:10.1016/j.cub.2020.04.002 · Cited by 64 · see citing works
Maixner, F., Sarhan, M. S., Huang, K. D., Tett, A., Schoenafinger, A., Zingale, S., Blanco-Míguez, A., Manghi, P., Cemper-Kiesslich, J., Rosendahl, W., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.09.031 · Cited by 62 · see citing works
Genomic analyses of hair from Ludwig van Beethoven
Begg, T. J. A., Schmidt, A., Kocher, A., Larmuseau, M., Runfeldt, G., Maier, P. A., Wilson, J. D., Barquera, R., Maj, C., Szolek, A., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.02.041 · Cited by 61 · see citing works
Toward high-resolution population genomics using archaeological samples
Морозова, И., Flegontov, P., Mikheyev, A. S., Bruskin, S. A., Asgharian, H., Пономаренко, П. М., Klyuchnikov, V., GaneshPrasad, A., Prokhortchouk, E., Gankin, Y. V., et al. (2016) · DNA Research · doi:10.1093/dnares/dsw029 · Cited by 58 · see citing works
He, Y. H., Jamieson, A., Hulme‐Beaman, A., Conroy, C. J., Knight, B., Speller, C., Al-Jarah, H., Eager, H., Trinks, A., Adikari, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30009-z · Cited by 57 · see citing works
Genetic admixture and language shift in the medieval Volga-Oka interfluve
Peltola, S., Majander, K., Makarov, N., Dobrovolskaya, M. V., Nordqvist, K., Salmela, E., & Onkamo, P. (2022) · Current Biology · doi:10.1016/j.cub.2022.11.036 · Cited by 60 · see citing works
Giffin, K. L., Lankapalli, A. K., Sabin, S. J., Spyrou, M. A., Posth, C., Kozakaitė, J., Friedrich, R., Miliauskienė, Ž., Jankauskas, R., Herbig, A., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-66012-x · Cited by 59 · see citing works
Seguin‐Orlando, A., Donat, R., Sarkissian, C. S. I. D., Southon, J. R., Thèves, C., Manen, C., Tchérémissinoff, Y., Crubézy, É., Shapiro, B., Deleuze, J., et al. (2021) · Current Biology · doi:10.1016/j.cub.2020.12.015 · Cited by 53 · see citing works
Neukamm, J., Pfrengle, S., Molak, M., Seitz, A., Francken, M., Eppenberger, P., Avanzi, C., Reiter, E., Urban, C., Welte, B., et al. (2020) · BMC Biology · doi:10.1186/s12915-020-00839-8 · Cited by 55 · see citing works
Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans
Racimo, F., Renaud, G., & Slatkin, M. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005972 · Cited by 52 · see citing works
Self-citationAdvancements and Challenges in Ancient DNA Research: Bridging the Global North–South Divide
Dalal, V., Pasupuleti, N., Chaubey, G., Rai, N., & Shinde, V. S. (2023) · Genes · doi:10.3390/genes14020479 · Cited by 55 · see citing works
Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX
Hanghøj, K., Seguin‐Orlando, A., Schubert, M., Madsen, T. L., Pedersen, J. S., Willerslev, E., & Orlando, L. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw184 · Cited by 53 · see citing works
Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes
Pfrengle, S., Neukamm, J., Guellil, M., Keller, M., Molak, M., Avanzi, C., Kushniarevich, A., Montes, N., Neumann, G. U., Reiter, E., et al. (2021) · BMC Biology · doi:10.1186/s12915-021-01120-2 · Cited by 52 · see citing works
Population Genetics and Signatures of Selection in Early Neolithic European Farmers
Childebayeva, A., Rohrlach, A. B., Barquera, R., Rivollat, M., Aron, F., Szolek, A., Kohlbacher, O., Nicklisch, N., Alt, K. W., Gronenborn, D., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac108 · Cited by 49 · see citing works
Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt
Rampelli, S., Turroni, S., Mallol, C., Gómez, C. M. H., Galván, B., Sistiaga, A., Biagi, E., Astolfi, A., Brigidi, P., Benazzi, S., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01689-y · Cited by 51 · see citing works
Neparáczki, E., Maróti, Z., Kalmár, T., Kocsy, K., Maár, K., Bihari, P., Nagy, I., Fóthi, E., Pap, I., Kustár, Á., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0205920 · Cited by 51 · see citing works
- Authors
- Renaud, G., Slon, V., Duggan, A. T., & Kelso, J.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- McMaster University (CA)
- Corresponding author
- Renaud, Gabriel
- Venue
- Genome Biology
- Published
- 2015-10-12
- Volume
- 16
- Issue
- 1
- Pages
- 224-224
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4601135
- OpenAlex
- W2099595226
- Cited by
- 509
- References
- 32
- Citations by year
- 2026: 63 · 2025: 78 · 2024: 57 · 2023: 60 · 2022: 40 · 2021: 60 · 2020: 60 · 2019: 34 · 2018: 28 · 2017: 19 · 2016: 10
- FWCI
- 12.98
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- Max Planck Digital Library (submittedVersion, other-oa)
- Funders
- Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (PGSD2-438066-2013)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- ancient DNA, contamination estimation, cytosine deamination, endogenous DNA, fragment size distribution
- MeSH terms
- Animals, Base Sequence, DNA, Mitochondrial, Humans, Software, Consensus Sequence, Sequence Analysis, DNA, Genome, Mitochondrial, DNA Contamination, 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
