DNA analysis of an early modern human from Tianyuan Cave, China
Open accessAbstract
Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.
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The study evaluated each individual for evidence of authentic ancient DNA by limiting to libraries with a minimum of 3% cytosine-to-thymine errors at the final nucleotide, requiring X-to-Y-chromosome ratio characteristic of sex, >95% matching to mtDNA consensus, and <2% contamination for males.
“We evaluated each individual for evidence of authentic ancient DNA by limiting to libraries with a minimum of 3% cytosine-to-thymine errors at the final nucleotide29, by requiring that the ratio of X-to-Y-chromosome sequences was characteristic of either a male or a female, by requiring >95% matching to the consensus sequence of mitochondrial DNA30, and by requiring (for males) a lack of variation”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [30]
The citation is attached to the cytosine-to-thymine error criterion. In Results and Discussion (page unavailable), the paper uses end-of-fragment substitutions as evidence of ancient DNA and reports frequencies of 25–30% close to fragment ends. It does not specify a minimum of 3% at the final nucleotide as a library-selection rule. (LLM, conf=0.84)
Experimental — accuracy not yet measuredWe assessed the quality of each library at the screening stage using three standard methods for determining ancient DNA authenticity: mitochondrial genome matching rate, C-to-T substitution rate, and X-chromosome contamination.
“We assessed the quality of each library at the screening stage using three standard methods for determining ancient DNA authenticity.”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [30]
The Results and Discussion section (“DNA Sequence Authenticity”; page unavailable) uses mitochondrial sequence agreement and C→T substitutions to assess whether DNA in the Tianyuan libraries is ancient and largely from one individual. Our copy does not describe X-chromosome contamination as a third method or say that these three methods were used to assess each library at screening. (LLM, conf=0.87)
Experimental — accuracy not yet measured
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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 · see citing works
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 · see citing works
MrBayes 3: Bayesian phylogenetic inference under mixed models
Ronquist, F., & Huelsenbeck, J. P. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg180 · Cited by 28,956 · see citing works
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820 · 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
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-citationReanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA
Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M., & Howell, N. (1999) · Nature Genetics · doi:10.1038/13779 · Cited by 3,337 · see citing works
Ancient Admixture in Human History
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848 · see citing works
Inference of population splits and mixtures from genome-wide allele frequency data
Pickrell, J. K., & Pritchard, J. K. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002967 · Cited by 2,731 · see citing works
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 · 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-citationGutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · cited 1× · see citing works
“Asian and European populations from nuclear DNA variation in present-day populations (34).”
BackgroundGnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1523 · Cited by 1,433 · cited 1× · see citing works
“(25) that uses oligonucleotides synthesized on arrays to construct probe libraries that are then amplified and converted into biotinylated RNA capture probes through in vitro transcription.”
BackgroundDouble indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
Kircher, M., Sawyer, S., & Meyer, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr771 · Cited by 1,106 · cited 2× · see citing works
“In addition, sample-specific barcodes were introduced into both library adaptors during amplification (35), which was performed using AmpliTaq Gold DNA polymerase (Applied Biosystems).”
MethodPatterns 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-citationCorrecting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock
Soares, P. A., Ermini, L., Thomson, N., Mormina, M., Rito, T., Röhl, A., Salas, A., Oppenheimer, S., Macaulay, V. A., & Richards, M. B. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.05.001 · Cited by 736 · see citing works
Genome-wide in situ exon capture for selective resequencing
Hodges, E. C., Xuan, Z., Balija, V. S., Kramer, M., Molla, M. N., Smith, S. W., Middle, C. M., Rodesch, M. J., Albert, T. J., Hannon, G. J., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.42 · Cited by 677 · see citing works
Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania
Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A. M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.09.005 · Cited by 656 · see citing works
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 601 · see citing works
Self-citationMultiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products
Maričić, T., Whitten, M., & Pääbo, S. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014004 · Cited by 566 · see citing works
Self-citationPhylogeographic Differentiation of Mitochondrial DNA in Han Chinese
Yao, Y., Kong, Q., Bandelt, H., Kivisild, T., & Zhang, Y.-P. (2002) · The American Journal of Human Genetics · doi:10.1086/338999 · Cited by 536 · see citing works
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 501 · see citing works
Self-citationRemoval of deaminated cytosines and detection of in vivo methylation in ancient DNA
Briggs, A. W., Stenzel, U., Meyer, M., Krause, J., Kircher, M., & Pääbo, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1163 · Cited by 491 · see citing works
Self-citationTemporal 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-citationThe emerging limbs and twigs of the East Asian mtDNA tree
Kivisild, T., Tolk, H.-V., Parik, J., Wang, Y., Papiha, S. S., Bandelt, H.-J., & Villems, R. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003996 · Cited by 403 · see citing works
Solid-phase reversible immobilization for the isolation of PCR products
DeAngelis, M. M., Wang, D. G., & Hawkins, T. L. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.22.4742 · Cited by 393 · see citing works
Kong, Q., Bandelt, H., Sun, C., Yao, Y., Salas, A., Achilli, A., Wang, C., Li, Z., Zhu, C., Wu, S., et al. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl130 · Cited by 391 · see citing works
Dabney, J., & Meyer, M. (2012) · BioTechniques · doi:10.2144/000113809 · Cited by 316 · see citing works
Self-citationA Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia
Krause, J., Briggs, A. W., Kircher, M., Maričić, T., Zwyns, N., Derevianko, A. P., & Pääbo, S. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.068 · Cited by 290 · see citing works
Self-citationTargeted Investigation of the Neandertal Genome by Array-Based Sequence Capture
Burbano, H. A., Hodges, E. C., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., Good, J. M., Maričić, T., Johnson, P. L. F., Xuan, Z., et al. (2010) · Science · doi:10.1126/science.1188046 · Cited by 276 · see citing works
Self-citationImproved 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 · see citing works
Self-citation(1995) · Europe PMC (PubMed Central) · Cited by 262 · see citing works
Soares, P. A., Achilli, A., Semino, O., Davies, W., Macaulay, V. A., Bandelt, H., Torroni, A., & Richards, M. B. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.054 · Cited by 243 · 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
(1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040240 · Cited by 236 · see citing works
European early modern humans and the fate of the Neandertals
Trinkaus, E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702214104 · Cited by 202 · see citing works
An early modern human from Tianyuan Cave, Zhoukoudian, China
Shang, H., Tong, H., Zhang, S., Chen, F., & Trinkaus, E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702169104 · Cited by 196 · see citing works
Anatomically modern human in Southeast Asia (Laos) by 46 ka
Demeter, F., Shackelford, L., Bacon, A., Duringer, P., Westaway, K., Sayavongkhamdy, T., Braga, J., Sichanthongtip, P., Khamdalavong, P., Ponche, J., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208104109 · Cited by 180 · see citing works
The Human Genetic History of the Americas: The Final Frontier
O’Rourke, D. H., & Raff, J. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.051 · Cited by 177 · see citing works
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 168 · see citing works
Addressing challenges in the production and analysis of illumina sequencing data
Kircher, M., Heyn, P. C., & Kelso, J. F. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-382 · Cited by 160 · see citing works
Self-citationThe Human Genetic History of East Asia: Weaving a Complex Tapestry
Stoneking, M., & Delfin, F. C. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.052 · Cited by 141 · see citing works
Ávila‐Arcos, M. C., Cappellini, E., Romero-Navarro, J. A., Wales, N., Moreno-Mayar, J. V., Rasmussen, M. A., Fordyce, S. L., Montiel, R., Vielle‐Calzada, J., Willerslev, E., et al. (2011) · Scientific Reports · doi:10.1038/srep00074 · Cited by 129 · see citing works
Past human migrations in East Asia : matching archaeology, linguistics and genetics
Sanchez‐Mazas, A. (2008) · doi:10.4324/9780203926789 · Cited by 126 · see citing works
Kumar, S., Bellis, C., Zlojutro, M., Melton, P. E., Blangero, J., & Curran, J. E. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-293 · Cited by 98 · 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-citationTong, H., Shang, H., Zhang, S., & Chen, F. (2004) · Chinese Science Bulletin · doi:10.1007/bf02889760 · Cited by 36 · see citing works
Tong, H. (2004) · Chinese Science Bulletin · doi:10.1360/03wd0561 · Cited by 12 · see citing works
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Research works printed but not linked: 1
- [3]Shang H, Trinkaus E. The Early Modern Human from Tianyuan Cave. College Station, TX: Texas A&M Univ Press; 2010. [Google Scholar]
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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-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-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
Genome-wide patterns of selection in 230 ancient Eurasians
Mathieson, I., Lazaridis, I., Rohland, N., Mallick, S., Patterson, N., Roodenberg, S. A., Harney, E., Stewardson, K., Fernandes, D., Novak, M., et al. (2015) · Nature · doi:10.1038/nature16152 · Cited by 1,515 · 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
“Because none of the sequences aligned to the mitochondrial genome of bear, we enriched the sequencing libraries for mitochondrial sequences using hybridization capture (22, 23).”
MethodSelf-citationAncient 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
“The WHG must then have split from eastern non-Africans >40,000 years ago, as this is the age of the Chinese Tianyuan sample which clusters with eastern non-Africans to the exclusion of Europeans 28 .”
Self-citationUpper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford Jr, T. W., Orlando, L., Metspalu, E., et al. (2014) · Nature · doi:10.1038/nature12736 · Cited by 963 · see citing works
Genomic insights into the origin of farming in the ancient Near East
Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C., Rohland, N., Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K., et al. (2016) · Nature · doi:10.1038/nature19310 · Cited by 955 · see citing works
“8 (4) What is the genetic contribution of these early Near Eastern farmers to later populations of the Near East?”
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
“Tianyuan 1301 [29] a 39,475 6 645 BA-03222 16,559 (99.”
InfluentialSelf-citationAncient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016) · Nature · doi:10.1038/nature16544 · Cited by 577 · 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-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 · 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 genome of the offspring of a Neanderthal mother and a Denisovan father
Slon, V., Mafessoni, F., Vernot, B., de Filippo, C., Grote, S., Viola, B., Hajdinjak, M., Peyrégne, S., Nagel, S., Brown, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0455-x · Cited by 536 · see citing works
Self-citationSchubert, M., Ermini, L., Sarkissian, C. S. I. D., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernández, R., Kircher, M., McCue, M. E., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.063 · Cited by 515 · see citing works
“In addition, target-enrichment approaches have revealed a plethora of complete ancient mitochondrial genome sequences 27–35 , the sequence of the Neandertal exome 36 , a complete chromosome of an ~50,000-year-old human from China 31 and the complete genome sequence of microbial pathogens responsible for massive histor…”
BackgroundSeparating 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
“We used the calmd program in the samtools (6) suite to recompute the MD field (containing alignment information, such as mismatches) for all datasets.”
MethodInfluentialA late Middle Pleistocene Denisovan mandible from the Tibetan Plateau
Chen, F., Welker, F., Shen, C., Bailey, S. E., Bergmann, I., Davis, S. A., Xia, H., Wang, H., Fischer, R., Freidline, S. E., et al. (2019) · Nature · doi:10.1038/s41586-019-1139-x · Cited by 498 · see citing works
Self-citationAncient DNA indicates human population shifts and admixture in northern and southern China
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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-citationAncient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas
Llamas, B., Fehren‐Schmitz, L., Valverde, G., Soubrier, J., Mallick, S., Rohland, N., Nordenfelt, S., Valdiosera, C. E., Richards, S. M., Rohrlach, A. B., et al. (2016) · Science Advances · doi:10.1126/sciadv.1501385 · Cited by 400 · see citing works
Parallel palaeogenomic transects reveal complex genetic history of early European farmers
Lipson, M., Szécsényi-Nagy, A., Mallick, S., Pósa, A., Stégmár, B., Keerl, V., Rohland, N., Stewardson, K., Ferry, M., Michel, M., et al. (2017) · Nature · doi:10.1038/nature24476 · Cited by 389 · see citing works
The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes
Mallick, S., Micco, A., Mah, M., Ringbauer, H., Lazaridis, I., Olalde, Í., Patterson, N. J., & Reich, D. (2024) · Scientific Data · doi:10.1038/s41597-024-03031-7 · Cited by 438 · see citing works
Rohland, N., Glocke, I., Aximu‐Petri, A., & Meyer, M. (2018) · Nature Protocols · doi:10.1038/s41596-018-0050-5 · Cited by 358 · see citing works
Self-citationCarpenter, M. L., Buenrostro, J. D., Valdiosera, C. E., Schroeder, H., Allentoft, M. E., Sikora, M., Rasmussen, M. A., Gravel, S., Guillén, S. E., Nekhrizov, G., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.002 · Cited by 322 · see citing works
“With regard to the data generated, the most similar method to WISC for aDNA capture is chromosome 21 capture.(8) That method was performed on libraries from a single specimen from the Tianyuan Cave in China that contained 0.”
BackgroundMethodAncient pathogen genomics as an emerging tool for infectious disease research
Spyrou, M. A., Bos, K. I., Herbig, A., & Krause, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0119-1 · Cited by 313 · see citing works
Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico
Vågene, Å. J., Herbig, A., Campana, M. G., García, N. M. R., Warinner, C., Sabin, S. J., Spyrou, M. A., Valtueña, A. A., Huson, D. H., Tuross, N., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0446-6 · Cited by 307 · 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
Self-citationOrigins and genetic legacy of prehistoric dogs
Bergström, A., Frantz, L., Schmidt, R., Ersmark, E., Lebrasseur, O., Girdland-Flink, L., Lin, A. T., Storå, J., Sjögren, K.-G., Anthony, D., et al. (2020) · Science · doi:10.1126/science.aba9572 · Cited by 297 · see citing works
Genomic 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
Early Austronesians: Into and Out Of Taiwan
Ko, A. M., Chen, C., Fu, Q., Delfin, F. C., Li, M., Chiu, H.-L., Stoneking, M., & Ko, Y. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.02.003 · Cited by 306 · see citing works
Self-citationChimpanzee genomic diversity reveals ancient admixture with bonobos
de Manuel, M., Kuhlwilm, M., Frandsen, P., Sousa, V. C., Desai, T., Prado-Martinez, J., Hernández-Rodríguez, J., Dupanloup, I., Lao, Ó., Hallast, P., et al. (2016) · Science · doi:10.1126/science.aag2602 · Cited by 297 · 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
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
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
Reconstructing ancient genomes and epigenomes
Orlando, L., Gilbert, M. T. P., & Willerslev, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3935 · Cited by 279 · see citing works
Reducing Microbial and Human Contamination in DNA Extractions from Ancient Bones and Teeth
Korlević, P., Gerber, T., Gansauge, M.-T., Hajdinjak, M., Nagel, S., Aximu‐Petri, A., & Meyer, M. (2015) · BioTechniques · doi:10.2144/000114320 · Cited by 267 · see citing works
Self-citationPalaeogenomics 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
“…of human DNA in shot-gun data around 0.1% or greater were enriched for a set of 1,237,207 targeted SNPs (1240k capture) across the human genome 6 . mtDNA capture 63 was also performed for those libraries where mtDNA coverage was not high enough to assess mtDNA haplogroup and contamination.”
InfluentialAncient genomes link early farmers from Atapuerca in Spain to modern-day Basques
Günther, T., Valdiosera, C., Malmström, H., Ureña, I., Rodriguez-Varela, R., Sverrisdóttir, Ó. O., Daskalaki, E. A., Skoglund, P., Naidoo, T., Svensson, E. M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509851112 · Cited by 278 · see citing works
Toward a new history and geography of human genes informed by ancient DNA
Pickrell, J. K., & Reich, D. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.07.007 · Cited by 271 · see citing works
“This strategy was used to obtain a high-quality mitochondrial genome sequence from a 400 000 year old archaic human [127], as well as approximately twofold redundant coverage of chromosome 21 from the 40 000 year old Tianyuan sample from northern China [110].”
InfluentialPatterns of coding variation in the complete exomes of three Neandertals
Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405138111 · Cited by 247 · see citing works
“Results and Discussion We used densely tiled oligonucleotide probes (9) and a recently described protocol (11) to capture the protein-coding exons from 17,367 genes in a ∼49,000-y-old (12) (uncalibrated radiocarbon date) Neandertal from Spain (SD1253, El Sidrón Cave) and a ∼44,000-y-old (uncalibrated radiocarbon date)…”
MethodSelf-citationReconstructing the genetic history of late Neanderthals
Hajdinjak, M., Fu, Q., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Skoglund, P., Narasimham, V., Rougier, H., Crèvecoeur, I., et al. (2018) · Nature · doi:10.1038/nature26151 · Cited by 258 · see citing works
Self-citationSlatkin, M., & Racimo, F. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1524306113 · Cited by 252 · see citing works
Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau
Zhang, D., Xia, H., Chen, F., Li, B., Slon, V., Cheng, T., Yang, R., Jacobs, Z. L., Dai, Q., Massilani, D., et al. (2020) · Science · doi:10.1126/science.abb6320 · Cited by 252 · see citing works
Self-citationHigher Levels of Neanderthal Ancestry in East Asians than in Europeans
Wall, J. D., Yang, M. A., Jay, F., Kim, S. K., Durand, E. Y., Stevison, L. S., Gignoux, C., Woerner, A., Hammer, M. F., & Slatkin, M. (2013) · Genetics · doi:10.1534/genetics.112.148213 · Cited by 249 · see citing works
“The eight populations are Utah residents with Northern and Western European ancestry from the CEPH collection (CEU); Han Chinese from Beijing, China (CHB); Gujarati Indians from Houston (GIH); Japanese from Tokyo (JPT); Luhya from Webuye, Kenya (LWK); Maasai from Kinyawa, Kenya (MKK); Toscani from Italy (TSI); and Yor…”
BackgroundInfluentialPleistocene 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
Self-citation40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia
Yang, M. A., Gao, X., Theunert, C., Tong, H., Aximu‐Petri, A., Nickel, B., Slatkin, M., Meyer, M., Pääbo, S., Kelso, J. F., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.09.030 · Cited by 237 · see citing works
Self-citationLanguage 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
The deep population history of northern East Asia from the Late Pleistocene to the Holocene
Mao, X., Zhang, H., Qiao, S., Liu, Y., Chang, F., Xie, P., Zhang, M., Wang, T., Li, M., Cao, P., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.040 · Cited by 234 · see citing works
Self-citationLarge-scale migration into Britain during the Middle to Late Bronze Age
Patterson, N. J., Isakov, M., Booth, T. J., Büster, L., Fischer, C.-É., Olalde, Í., Ringbauer, H., Akbari, A., Cheronet, O., Bleasdale, M., et al. (2021) · Nature · doi:10.1038/s41586-021-04287-4 · Cited by 237 · see citing works
Ancient Genomics of Modern Humans: The First Decade
Skoglund, P., & Mathieson, I. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021749 · Cited by 246 · see citing works
O’Connell, J., & Allen, J. (2015) · Journal of Archaeological Science · doi:10.1016/j.jas.2015.02.020 · Cited by 228 · see citing works
“…of modern and fossil human mitochondrial (mt) DNA, still the best characterized locus for dating humanmigrations (e.g. Endicott et al., 2009; Soares et al., 2009, 2012; Behar et al., 2012; Fernandes et al., 2012; Henn et al., 2012; Fu et al., 2013b; Mellars et al., 2013b; Rito et al., 2013).”
BackgroundGansauge, M.-T., Aximu‐Petri, A., Nagel, S., & Meyer, M. (2020) · Nature Protocols · doi:10.1038/s41596-020-0338-0 · Cited by 222 · see citing works
Self-citationLlamas, 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
A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA
Shapiro, B., & Hofreiter, M. (2014) · Science · doi:10.1126/science.1236573 · Cited by 220 · see citing works
Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry
Hajdinjak, M., Mafessoni, F., Skov, L., Vernot, B., Hübner, A., Fu, Q., Essel, E., Nagel, S., Nickel, B., Richter, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03335-3 · Cited by 217 · see citing works
Self-citationPaleolithic 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
“pestis captures of both full-UDG and partially-UDG-treated libraries were performed using a published protocol (Fu et al., 2013), adapted for Y.”
Human population history at the crossroads of East and Southeast Asia since 11,000 years ago
Wang, T., Wang, W., Xie, G., Li, Z., Fan, X., Yang, Q., Wu, X., Cao, P., Liu, Y., Yang, R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.018 · Cited by 212 · see citing works
Self-citationEmergence and diversity of modern human behavior in Paleolithic Asia
(2015) · Choice Reviews Online · doi:10.5860/choice.190813 · Cited by 213 · see citing works
Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe
Lamnidis, T. C., Majander, K., Jeong, C., Salmela, E., Wessman, A., Moiseyev, V. G., Khartanovich, V. I., Balanovsky, O. P., Ongyerth, M., Weihmann, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07483-5 · Cited by 205 · see citing works
Self-citationAge estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave
Douka, K., Slon, V., Jacobs, Z. L., Ramsey, C. B., Shunkov, M. V., Derevianko, A. P., Mafessoni, F., Kozlikin, M. B., Li, B., Grün, R., et al. (2019) · Nature · doi:10.1038/s41586-018-0870-z · Cited by 203 · see citing works
Self-citationA Robust Framework for Microbial Archaeology
Warinner, C., Herbig, A., Mann, A. E., Yates, J. A. F., Weiß, C. L., Burbano, H. A., Orlando, L., & Krause, J. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091416-035526 · Cited by 194 · see citing works
“This technique can be performed either on chip (20) or in solution (9, 52), and the goal is to remove unwanted DNA from a sample prior to sequencing.”
BackgroundSelf-citationAncient DNA reveals a multistep spread of the first herders into sub-Saharan Africa
Prendergast, M. E., Lipson, M., Sawchuk, E., Olalde, Í., Ogola, C. A., Rohland, N., Sirak, K. A., Adamski, N., Bernardos, R. L., Broomandkhoshbacht, N., et al. (2019) · Science · doi:10.1126/science.aaw6275 · Cited by 196 · 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
Late Pleistocene archaic human crania from Xuchang, China
Li, Z., Wu, X., Zhou, L., Liu, W., Gao, X., Nian, X., & Trinkaus, E. (2017) · Science · doi:10.1126/science.aal2482 · Cited by 203 · see citing works
Self-citationThe Demographic Development of the First Farmers in Anatolia
Kılınç, G. M., Omrak, A., Özer, F., Günther, T., Büyükkarakaya, A. M., Bıçakçı, E., Baird, D., Dönertaş, H. M., Ghalichi, A., Yaka, R., et al. (2016) · Current Biology · doi:10.1016/j.cub.2016.07.057 · Cited by 190 · see citing works
The evolutionary history of Neanderthal and Denisovan Y chromosomes
Petr, M., Hajdinjak, M., Fu, Q., Essel, E., Rougier, H., Crèvecoeur, I., Semal, P., Golovanova, L. V., Doronichev, V. B., Lalueza‐Fox, C., et al. (2020) · Science · doi:10.1126/science.abb6460 · Cited by 196 · see citing works
Self-citationThe genetic history of the Southern Arc: A bridge between West Asia and Europe
Lazaridis, I., Alpaslan-Roodenberg, S., Acar, A., Açıkkol, A., Agelarakis, A. P., Aghikyan, L., Akyüz, U., Andreeva, D., Andrijašević, G., Antonović, D., et al. (2022) · Science · doi:10.1126/science.abm4247 · Cited by 194 · see citing works
Craniometrics Reveal “Two Layers” of Prehistoric Human Dispersal in Eastern Eurasia
Matsumura, H., Hung, H., Higham, C. F., Zhang, C., Yamagata, M., Nguyen, L. C., Li, Z., Fan, X., Simanjuntak, T., Oktaviana, A. A., et al. (2019) · Scientific Reports · doi:10.1038/s41598-018-35426-z · Cited by 191 · see citing works
Harnessing ancient genomes to study the history of human adaptation
Marciniak, S., & Perry, G. H. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.65 · Cited by 182 · see citing works
“Fu et al.(171) 2013 1 1 Chromosome 21 capture South and central Asia 1”
BackgroundThe makers of the Protoaurignacian and implications for Neandertal extinction
Benazzi, S., Slon, V., Talamo, S., Negrino, F., Peresani, M., Bailey, S. E., Sawyer, S., Panetta, D., Vicino, G., Starnini, E., et al. (2015) · Science · doi:10.1126/science.aaa2773 · Cited by 185 · see citing works
Self-citationHunter-Gatherers and the Origins of Religion
Peoples, H. C., Duda, P., & Marlowe, F. W. (2016) · Human Nature · doi:10.1007/s12110-016-9260-0 · Cited by 186 · see citing works
“Pleistocene hunter-gatherers would most likely have possessed both the cognitive and communicative skills to share religious beliefs and practices prior to dispersal out of Africa more than 60 kya (Fu et al. 2013; Henn et al. 2012; Johansson 2011; Lind et al. 2013).”
BackgroundBrown, S., Higham, T., Slon, V., Pääbo, S., Meyer, M., Douka, K., Brock, F., Comeskey, D. J., Procopio, N., Shunkov, M. V., et al. (2016) · Scientific Reports · doi:10.1038/srep23559 · Cited by 183 · see citing works
Self-citationThe 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
Ancient West African foragers in the context of African population history
Lipson, M., Ribot, I., Mallick, S., Rohland, N., Olalde, Í., Adamski, N., Broomandkhoshbacht, N., Lawson, A. M., López, S., Oppenheimer, J., et al. (2020) · Nature · doi:10.1038/s41586-020-1929-1 · Cited by 173 · see citing works
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genomePreprint
Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., et al. (2013) · Genome Research · doi:10.1101/gr.163592.113 · Cited by 171 · see citing works
The Stone Age Plague and Its Persistence in Eurasia
Valtueña, A. A., Mittnik, A., Key, F. M., Haak, W., Allmäe, R., Belinskij, A. B., Daubaras, M., Feldman, M., Jankauskas, R., Janković, I., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.10.025 · Cited by 169 · see citing works
Population Turnover in Remote Oceania Shortly after Initial Settlement
Lipson, M., Skoglund, P., Spriggs, M., Valentin, F., Bedford, S., Shing, R., Buckley, H. R., Phillip, I., Ward, G. K., Mallick, S., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.02.051 · Cited by 171 · see citing works
A high-resolution picture of kinship practices in an Early Neolithic tomb
Fowler, C., Olalde, Í., Cummings, V., Armit, I., Büster, L., Cuthbert, S., Rohland, N., Cheronet, O., Pinhasi, R., & Reich, D. (2021) · Nature · doi:10.1038/s41586-021-04241-4 · Cited by 167 · see citing works
Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments
Vernot, B., Zavala, E. I., Gómez‐Olivencia, A., Jacobs, Z. L., Slon, V., Mafessoni, F., Romagné, F., Pearson, A., Petr, M., Sala, N., et al. (2021) · Science · doi:10.1126/science.abf1667 · Cited by 161 · see citing works
Self-citationBeringia and the global dispersal of modern humans
Hoffecker, J. F., Elias, S. A., O’Rourke, D. H., Scott, G. R., & Bigelow, N. H. (2016) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21478 · Cited by 161 · see citing works
Ancient DNA and deep population structure in sub-Saharan African foragers
Lipson, M., Sawchuk, E., Thompson, J. C., Oppenheimer, J., Tryon, C. A., Ranhorn, K. L., de Luna, K. M., Sirak, K. A., Olalde, Í., Ambrose, S. H., et al. (2022) · Nature · doi:10.1038/s41586-022-04430-9 · Cited by 154 · see citing works
Keller, M., Spyrou, M. A., Scheib, C. L., Neumann, G. U., Kröpelin, A., Haas-Gebhard, B., Päffgen, B., Haberstroh, J., Lacomba, A. R. I., Raynaud, C., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1820447116 · Cited by 159 · see citing works
“The capture was performed as previously described (62) on 96604 well plates with a maximum of two samples pooled per well and all blanks with unique index 605”
Inferences from tip‐calibrated phylogenies: a review and a practical guide
Rieux, A., & Balloux, F. (2016) · Molecular Ecology · doi:10.1111/mec.13586 · Cited by 149 · see citing works
The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomesPreprint
Mallick, S., Micco, A., Mah, M., Ringbauer, H., Lazaridis, I., Olalde, Í., Patterson, N. J., & Reich, D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.06.535797 · Cited by 153 · see citing works
“2015 with the advent of large-scale studies of Holocene genomes, in-solution enrichment of ancient DNA libraries for targeted single nucleotide polymorphisms (SNPs) [4-6] and the introduction of automated protocols and liquid handling robots for processing of ancient DNA libraries [7, 8], that the number of individual…”
BackgroundThe impact of whole-genome sequencing on the reconstruction of human population history
Veeramah, K. R., & Hammer, M. F. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3625 · Cited by 148 · see citing works
A working model of the deep relationships of diverse modern human genetic lineages outside of Africa
Lipson, M., & Reich, D. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw293 · Cited by 145 · see citing works
“The former includes present-day East Asians and had differentiated as early as the 40 kya Tianyuan individual (Fu et al. 2013), while early members of the latter include ancient European hunter-gatherers (Lazaridis et al.”
BackgroundThree assays for in-solution enrichment of ancient human DNA at more than a million SNPsPreprint
Rohland, N., Mallick, S., Mah, M., Maier, R., Patterson, N. J., & Reich, D. (2022) · Genome Research · doi:10.1101/gr.276728.122 · Cited by 142 · see citing works
“The baits were then cleaved, amplified, and biotinylated in preparation for enrichment (Fu et al. 2013).”
BackgroundMethodInfluentialAncient 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
“2 million SNPs was performed using a set of DNA capture probes [“1240k”, composed of SNP panels 1 and 2, as described elsewhere (45)] and two successive rounds of in-solution hybridization capture (75).”
MethodSelf-citationResolving the ancestry of Austronesian-speaking populations
Soares, P. A., Tréjaut, J., Rito, T., Cavadas, B., Hill, C., Eng, K. K., Mormina, M., Brandão, A., Fraser, R. M., Wang, T., et al. (2016) · Human Genetics · doi:10.1007/s00439-015-1620-z · Cited by 143 · see citing works
“Ancient DNA calibration is becoming a widely used approach (Ho et al. 2007), but estimates based on a single sequence are highly divergent and present large confidence intervals (Fu et al. 2013b).”
BackgroundInfluentialThe Hybrid Origin of “Modern” Humans
Ackermann, R., Mackay, A., & Arnold, M. L. (2015) · Evolutionary Biology · doi:10.1007/s11692-015-9348-1 · Cited by 142 · see citing works
“However, we now know that Neanderthals and Denisovans (and potentially other archaic lineages) are part of many peoples’ ancestry today, raising the question of whether it is valid to exclude them from our species.”
BackgroundInfluentialSarkissian, C. S. I. D., Allentoft, M. E., Ávila‐Arcos, M. C., Barnett, R., Campos, P. F., Cappellini, E., Ermini, L., Fernández, R., da Fonseca, R. R., Ginolhac, A., et al. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0387 · Cited by 144 · see citing works
The source of the Black Death in fourteenth-century central Eurasia
Spyrou, M. A., Musralina, L., Gnecchi‐Ruscone, G. A., Kocher, A., Borbone, P. G., Khartanovich, V. I., Buzhilova, A., Djansugurova, L., Bos, K. I., Kühnert, D., et al. (2022) · Nature · doi:10.1038/s41586-022-04800-3 · Cited by 147 · see citing works
- Authors
- Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S.
- Affiliations
- Max Planck Society (DE)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Max Planck Institute for Developmental Biology (DE)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-01-22
- Volume
- 110
- Issue
- 6
- Pages
- 2223-2227
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3568306
- OpenAlex
- W2149683346
- Cited by
- 608
- References
- 47
- Citations by year
- 2026: 27 · 2025: 52 · 2024: 45 · 2023: 45 · 2022: 45 · 2021: 78 · 2020: 64 · 2019: 35 · 2018: 49 · 2017: 43 · 2016: 38 · 2015: 35 · 2014: 34 · 2013: 17
- FWCI
- 27.40
- 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)
- Digital Commons - University of South Florida (University of South Florida) (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 › Genetics › Genetic diversity and population structure
- Keywords
- early modern humans, ancient DNA, mitochondrial genome, nuclear genome, chromosome 21, archaic admixture, Asian ancestry, Native American ancestry
- MeSH terms
- Animals, Base Sequence, China, Chromosomes, Human, Pair 21, DNA, Mitochondrial, Fossils, Genetics, Population, Humans, Molecular Sequence Data, Phylogeny, Sequence Homology, Nucleic Acid, Hominidae, Gene Library, Sequence Analysis, DNA, Asian People, History, Ancient, Phylogeography
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