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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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“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
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“Moreover, I am also intrigue why authors chose not to use neither Contamix (Fu et al. 2013) or Schmutzi (Renaud, Slon, Duggan and Kelso 2015) both software used previously by the Reich lab.”
MethodAncient DNA sheds light on the genetic origins of early Iron Age Philistines
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BackgroundExtending the spectrum of DNA sequences retrieved from ancient bones and teethPreprint
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Self-citationSlon, V., Viola, B., Renaud, G., Gansauge, M.-T., Benazzi, S., Sawyer, S., Hublin, J., Shunkov, M. V., Derevianko, A. P., Kelso, J. F., et al. (2017) · Science Advances · doi:10.1126/sciadv.1700186 · Cited by 116
Self-citationDetecting Polygenic Adaptation in Admixture Graphs
Racimo, F., Berg, J. J., & Pickrell, J. K. (2018) · Genetics · doi:10.1534/genetics.117.300489 · Cited by 118
“Our modeling framework suggests that selection operated before or early in the process of divergence among East Asian populations - whose earliest separation dates at least as far back as approximately 10 thousand years ago [42, 43, 44, 45] - because the signal is common to different East Asian populations (Han Chines…”
BackgroundGakuhari, T., Nakagome, S., Rasmussen, S., Allentoft, M. E., Sato, T. K., Korneliussen, T. S., Chuinneagáin, B. N., Matsumae, H., Koganebuchi, K., Schmidt, R., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-01162-2 · Cited by 121
Selective enrichment of damaged DNA molecules for ancient genome sequencing
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BackgroundMethodSelf-citationAncient 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 125
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 123
Extensive pedigrees reveal the social organization of a Neolithic community
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Earliest known human burial in Africa
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Bronze and Iron Age population movements underlie Xinjiang population history
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Self-citationLate Middle Pleistocene Levallois stone-tool technology in southwest China
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Self-citationAncient DNA reveals admixture history and endogamy in the prehistoric Aegean
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“Here, we chose to minimize batch effects and consistently generated in-solution hybridization enrichment data, consisting of ~1,2 million ancestry-informative positions (1240K capture) 28,43,80,81 from all samples with 0.1% human endogenous DNA or more.”
InfluentialUsing Ancient DNA to Understand Evolutionary and Ecological Processes
Orlando, L., & Cooper, A. (2014) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-120213-091712 · Cited by 104
Imputation of ancient human genomes
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Human genetic history on the Tibetan Plateau in the past 5100 years
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Self-citationHuman evolution: a tale from ancient genomes
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An abundance of developmental anomalies and abnormalities in Pleistocene people
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Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments
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Self-citationThe genetic origin of the Indo-Europeans
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“We later increased the number of targeted SNPs in our nuclear capture from about 390,000 (390k) 2,76 to about 1.24 million (1240k) 77 for libraries passing the mitochondrial capture with nuclear spike-in.”
InfluentialDid the Denisovans Cross Wallace's Line?
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Why we are not all multiregionalists now
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The Evolutionary Origin and Genetic Makeup of Domestic Horses
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“In horses, such approaches have been applied to only a limited number of loci (Vilstrup et al. 2013; Sarkissian et al. 2015), but recent procedures enable genotyping millions of loci genome wide (Fu et al. 2016), and even entire chromosomes (Fu et al. 2013) and genomes (Carpenter et al. 2013).”
BackgroundUnlocking the origins and biology of domestic animals using ancient DNA and paleogenomics
McHugo, G. P., Dover, M. J., & MacHugh, D. E. (2019) · BMC Biology · doi:10.1186/s12915-019-0724-7 · Cited by 102
Early presence of Homo sapiens in Southeast Asia by 86–68 kyr at Tam Pà Ling, Northern Laos
Freidline, S. E., Westaway, K., Joannes‐Boyau, R., Duringer, P., Ponche, J., Morley, M. W., Hernandez, V., McAllister-Hayward, M. S., McColl, H., Zanolli, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38715-y · Cited by 100
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“see also [20]).”
The study of human Y chromosome variation through ancient DNA
Kivisild, T. (2017) · Human Genetics · doi:10.1007/s00439-017-1773-z · Cited by 93
“Hybridization enrichment approach targeting chromosome 21 has been successfully applied on the ~40 thousand year-old (KYA) human remains from Tianyuan Cave outside Beijing, China (Fu et al. 2013) suggesting that similar approaches can be applied in the future also on accessible (non-ampliconic) regions of the Y chromo…”
BackgroundNeandertal versus Modern Human Dietary Responses to Climatic Fluctuations
Zaatari, S. E., Grine, F. E., Ungar, P. S., & Hublin, J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0153277 · Cited by 90
The history and evolution of the Denisovan- EPAS1 haplotype in Tibetans
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“This work provides a timing estimate of the East Asian-specific Denisovan introgression, which we inferred at around 48 ka, and is consistent with archaeological evidence showing Denisovan ancestry in modern human individuals from 34 to 40 ka (59, 60).”
ResultA minimally destructive protocol for DNA extraction from ancient teethPreprint
Harney, É., Cheronet, O., Fernandes, D., Sirak, K. A., Mah, M., Bernardos, R. L., Adamski, N., Broomandkhoshbacht, N., Callan, K. A., Lawson, A. M., et al. (2021) · Genome Research · doi:10.1101/gr.267534.120 · Cited by 100
“…in the number of ancient genomes published each year (Slatkin and Racimo 2016) as a consequence of advances in ancient DNA sampling (Gamba et al. 2014; Damgaard et al. 2015), extraction (Dabney et al. 2013a; Rohland et al. 2018), and enrichment (Carpenter et al. 2013; Fu et al. 2013) techniques.”
BackgroundMethodA partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan
Kanzawa‐Kiriyama, H., Kryukov, K. A., Jinam, T. A., Hosomichi, K., Saso, A., Suwa, G., Ueda, S., Yoneda, M., Tajima, A., Shinoda, K., et al. (2016) · Journal of Human Genetics · doi:10.1038/jhg.2016.110 · Cited by 87
The Genomic History of the Bronze Age Southern Levant
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Human Dispersal from Siberia to Beringia
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“The early modern human from Tianyuan Cave, China.”
BackgroundInfluentialArchaic human remains from Hualongdong, China, and Middle Pleistocene human continuity and variation
Wu, X.-J., Pei, S., Cai, Y., Tong, H.-W., Li, Q., Dong, Z., Sheng, J.-C., Jin, Z.-T., DONGDONG, Xing, S., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1902396116 · Cited by 88
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Mosaic dental morphology in a terminal Pleistocene hominin from Dushan Cave in southern China
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“…803–815 https://doi.org/10.15184/aqy.2018.70 by cheaper sequencing, more efficient DNA-extraction and -preparation techniques, and new enrichment methods that restrict analysis to informative parts of the genome (Meyer & Kircher 2010; Meyer et al. 2012; Dabney et al. 2013; Fu et al. 2013, 2015).”
MethodInfluentialThe diverse genetic origins of a Classical period Greek army
Reitsema, L. J., Mittnik, A., Kyle, B., Catalano, G., Fabbri, P. F., Kazmi, A. C. S., Reinberger, K. L., Sìneo, L., Vassallo, S., Bernardos, R. L., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2205272119 · Cited by 83
“2 million single-nucleotide polymorphisms (SNPs) (47, 48) (Dataset S1).”
MethodNuclear 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
Self-citationGenome-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 81
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Reevaluating the timing of Neanderthal disappearance in Northwest Europe
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“To explore this, we extracted DNA from Spy 572a (25), constructed libraries (26), and performed hybridization capture (27) to test for the presence of ancient hominin and other mammalian mitochondrial DNA (mtDNA).”
MethodSelf-citationMicrobial Genomics of Ancient Plagues and Outbreaks
Andam, C. P., Worby, C. J., Chang, Q., & Campana, M. G. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.08.004 · Cited by 77
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Perspectives in polycystic ovary syndrome: From hair to eternity
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“Furthermore, the findings have evolutionary implications suggesting that the susceptibility loci shared between the Han Chinese and European PCOS are conserved because the ancestral Eurasian population migrated out of Africa approximately 100 000 years ago and these populations diverged 40 000 years ago (71, 118).”
BackgroundThe easternmost Middle Paleolithic (Mousterian) from Jinsitai Cave, North China
Li, F., Kuhn, S. L., Chen, F., Wang, Y., Southon, J. R., Peng, F., Shan, M., Wang, C., Ge, J., Wang, X., et al. (2017) · Journal of Human Evolution · doi:10.1016/j.jhevol.2017.10.004 · Cited by 80
Self-citationPalaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution
Meyer, M., Palkopoulou, E., Baleka, S., Stiller, M., Penkman, K. E. H., Alt, K. W., Ishida, Y., Mania, D., Mallick, S., Meijer, T., et al. (2017) · eLife · doi:10.7554/elife.25413 · Cited by 75
“Single-stranded biotinylated DNA probes were generated as described elsewhere (Fu et al., 2013) and used for two successive rounds of hybridization capture following a bead-based protocol (Maricic et al., 2010).”
MethodSelf-citationThe shaping of human diversity: filters, boundaries and transitions
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Human population dynamics and Yersinia pestis in ancient northeast Asia
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Human auditory ossicles as an alternative optimal source of ancient DNAPreprint
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“…driven largely by advances in isolating (Dabney et al. 2013; Rohland et al. 2018), preparing (Gansauge et al. 2017; Rohland et al. 2015), enriching (Fu et al. 2013, 2015; Haak et al. 2015; Mathieson et al. 2015), sequencing (Margulies et al. 2005), and analyzing (Briggs et al. 2007; Briggs et al.…”
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“Modern humans were present in China by at least 40 ka (Fu et al., 2013), with fragmentary human fossils showing some modern characters also recorded from the initial Late Pleistocene >100 ka (Liu et al.”
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Self-citationOrigin and Health Status of First-Generation Africans from Early Colonial Mexico
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“Calibration with fossil genomes has now served to constrain these rates for the recent human lineage (Fu et al., 2013b, 2014; Rieux et al., 2014).”
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Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens
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Human evolutionary history in Eastern Eurasia using insights from ancient DNA
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New Perspectives in Southeast Asian and Pacific Prehistory
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Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations
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“The printed probes were cleaved off the array, biotinylated, and prepared for capture according to Fu, et al. 86 .”
InfluentialGenetic admixture and language shift in the medieval Volga-Oka interfluve
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Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns
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“These methods used restriction enzymes that cut motifs occurring preferentially in contaminant DNA [16], enriched for endogenous DNA fragments via hybridization capture [28] or depleted contaminant DNA prior to DNA extraction [29, 30].”
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A male Denisovan mandible from Pleistocene Taiwan
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The earliest Denisovans and their cultural adaptation
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Self-citationThree Phases of Ancient Migration Shaped the Ancestry of Human Populations in Vanuatu
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One of the key characteristics of ancient DNA, low copy number, may be a product of its extraction
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Metadata
- 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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