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The complete genome sequence of a Neanderthal from the Altai Mountains
Open accessAbstract
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
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In the citing paper
“Genomic analyses have revealed that present-day non-African human populations inherit 1–4% of their genetic ancestry from introgression with Neanderthals (Green et al., 2010; Prüfer et al., 2014).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Prüfer et al., 2014
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
“Moreover, the introgressing Neanderthals were probably from populations that were separated both in time and space from the three archaic individuals who have so far been sequenced to high coverage-hereafter referred to as DAV (Denisovan, Altai Neanderthal and Vindija Neanderthal) 1,17,18 .”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [18]
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
“Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum.”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [14]
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
“In particular, non-African populations show 1% to 2% of Neanderthal ancestry in their genomes (Green et al. 2010; Prüfer et al. 2014) and Melanesians and East Asians display 3% and 0.2%, respectively, from Denisovans ancestry (Green et al. 2010; Meyer et al. 2012; Prüfer et al. 2014).”
From The Human Accelerated Region HAR202 Controls NPAS3 Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Prüfer et al. 2014
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
“West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, which could be explained if West Eurasians (but not East Asians) have partial ancestry from a source diluting their Neanderthal inheritance22.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [19]
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“Supporting this theory, we observe a negative correlation between Basal Eurasian ancestry and the rate of shared alleles with Neanderthals19 (Supplementary Information, section 5; Fig. 2).”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [19]
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
“This approach has revealed that archaic hominin populations survived extinction over long periods of time despite highly reduced effective population sizes [8][9][10] .”
From Ancient DNA analysis (2021) · cites this paper as [8]
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In the citing paper
“The mapping approaches employed in this study are consistent with those used in previous research [2, 6].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [2]
The cited source says what the claim attributes to it.
In the citing paper
“Evidence for super-archaic introgression into the ancestors of the Altai Denisovans 30 and, possibly, Andamanese populations 31-33 , suggests that viable reproduction may actually have been possible, though further evaluation of these hypotheses at present is not possible given the available data.”
From Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture (2021) · cites this paper as [30]
The cited source says what the claim attributes to it.
In the citing paper
“Analyses of the genomes of Neandertals and modern humans show that they encountered each other outside Africa and interbred [6, 15, 16].”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [15]
The cited source says what the claim attributes to it.
In the citing paper
“After modern humans left Africa more than 60,000 years ago, genetic evidence suggests multiple admixture events ~55,000 years [9] between modern humans and now extinct archaic humans including Neandertals [10–12] and Denisovans [13, 14].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“Both archaic genomes revealed evidence of admixture amongst various hominin lineages 8 , in which Neanderthals and Denisovans contributed significant ancestry to modern non-African populations and modern populations of Australasia and Oceania, respectively 221 , contributing to potential phenotypic and health consequences today 250 .”
From Ancient DNA analysis (2021) · cites this paper as [8]
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The resulting lower efficacy of selection allowed the accumulation of weakly deleterious alleles in Neanderthal populations31.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [31]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“It is striking that the highest estimates of Basal Eurasian ancestry are from the Near East, given the hypothesis that it was there that most admixture between Neanderthals and modern humans occurred19,23.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [19]
Experimental — accuracy not yet measuredIn the citing paper
“Neanderthal ancestry in all present-day non-Africans is estimated to be 1.5–2.1 % [14].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“the Neanderthal-derived DNA in all non-Africans is more closely related to a Neanderthal from the Caucasus than it is to either the Neanderthal from Siberia or the Neanderthal from Croatia [14]”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“A low level (~0.2 %) of Denisovan ancestry is also found across Eastern Eurasia and in Native American populations [14]”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“providing more evidence that archaic admixture occurred in West Asia early during modern humans’ exit from Africa.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“Denisovans themselves appear to have received gene flow from other archaic humans.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“It has been estimated that at least 0.5 % of the Denisovan genome was contributed by Neanderthals”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“and that 0.5–8 % comes from an unknown hominin who split from other hominins between 1.1 and 4 million ya [14].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“This conclusion is surprising because modern human ancestors and archaic hominins evolved separately for 550,000–765,000 years [14]”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [14]
In the citing paper
“The centrosome-associated cell division machinery contains at least three more proteins that carry modern human-specific amino-acid substitutions. CASC5 (cancer susceptibility candidate 5), KIF18A (kinesin family member 18A), and SPAG5 (sperm-associated antigen 5) localize to the mitotic spindle, which is organized by the centrosome, or to the kinetochore, which attaches chromosomes to the spindle”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Prufer et al., 2014
In the citing paper
“Prüfer et al. (22) used a similar technique to quantify divergence between archaic and modern genomes and found that branch length differences between sequencing batches often exceeded branch length differences between populations.”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [22]
In the citing paper
“A significant intersection was found with the data from Prüfer et al. [44] (p < 0.05) and with the combined data from Prüfer et al. [44] and Racimo [48] (p < 0.05).”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
In the citing paper
“CBL is located in a region showing signals of a strong selective sweep in AMH compared to Altai Neanderthals [44]”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
In the citing paper
“ERBB4 is one of many neural crest-related genes associated with selective signals in AMH (e.g., SNAI2 [44], CITED2 [44], PRDM10 [46, 78], and others [38]), some of which show fixed or nearly fixed amino acid changes compared to Neanderthals.”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
In the citing paper
“A significant intersection was found with the data in [44] (a = 691, b = 108, v = 9; p < 0.05) and with the combined data from [44] and [48] (a = 691, b = 419, v = 24, p < 0.05).”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [44]
In the citing paper
“Others, like RB1CC120 or PRDM10 and NCOA633 have been found in selective sweep screens, suggesting contributions of individual transcription factors, rather than the whole class of proteins.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
In the citing paper
“These genotype calls are absent from the files provided for the three archaic genomes due to different genotype calling and filtering procedures compared to the original publication of the Altai Neanderthal genome20,21.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
In the citing paper
“Among the 15 fixed protein-coding changes identified here but absent from previous analyses1,20, some might have also contributed to complex modifications of pathways in cell division, like AHR65 or DNHD166 (Supplementary Information 1), as well as other genes with HHMCs, like CHEK167 or the gene encoding for the protein TOP2A68, which shows the largest number of interactions with other HHMC-carry”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
In the citing paper
“It has been claimed20 that genes with fixed non-synonymous changes in humans are also more often expressed in the ventricular zone of the developing neocortex, compared to fixed synonymous changes.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
In the citing paper
“It has been proposed previously that protein-coding changes in cell cycle-related genes are highly relevant candidates for human-specific traits1,20, with the brain being specifically sensitive to such changes61.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [20]
In the citing paper
“Based on the observed general concordance between the selection time estimates and aDNA evidences, we developed an overall chronicle of human genome adaptation that is based on PS signals, the three AMH aDNA genomes and the Neanderthal genome consensus 40 (Fig. 4).”
From A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years (2015) · cites this paper as [40]
In the citing paper
“Although it is possible that a subset of sites are mis-labeled due to error, incomplete lineage sorting, and the divergence between introgressing and sequenced Neandertal genomes [14], this approach enriches for alleles of Neandertal origin.”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [14]
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Metadata
- Authors
- Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J. C., Vohr, S. H., Green, R. E., Hellmann, I., Johnson, P. L. F., Blanche, H., Cann, H., Kitzman, J. O., Shendure, J., Eichler, E. E., Lein, E. S., Bakken, T. E., Golovanova, L. V., Doronichev, V. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- University of California, Berkeley (US)
- Broad Institute (US)
- University of Washington (US)
- Chinese Academy of Sciences (CN)
- Harvard University (US)
- National Institutes of Health (US)
- University of California, Santa Cruz (US)
- Max Perutz Labs (AT)
- Emory University (US)
- Fondation Jean Dausset-CEPH (FR)
- Howard Hughes Medical Institute (US)
- Allen Institute for Brain Science (US)
- Russian Academy of Sciences (RU)
- Corresponding author
- Slatkin, Montgomery
- Reich, David
- Pääbo, Svante
- ORCID
- Prüfer, Kay
- Racimo, Fernando
- Patterson, Nick
- Jay, Flora
- Sankararaman, Sriram
- Sawyer, Susanna
- Renaud, Gabriel
- Sudmant, Peter H.
- Li, Heng
- Mallick, Swapan
- Dannemann, Michael
- Fu, Qiaomei
- Kircher, Martin
- Kuhlwilm, Martin
- Lachmann, Michael
- Meyer, Matthias
- Moorjani, Priya
- Mullikin, James C.
- Vohr, Samuel H.
- Green, Richard E.
- Hellmann, Ines
- Kitzman, Jacob O.
- Shendure, Jay
- Eichler, Evan E.
- Lein, Ed S.
- Bakken, Trygve E.
- Golovanova, Liubov V.
- Doronichev, Vladimir B.
- Shunkov, Michael V.
- Viola, Bence
- Slatkin, Montgomery
- Reich, David
- Kelso, Janet
- Pääbo, Svante
- Venue
- Nature
- Published
- 2013-12-18
- Volume
- 505
- Issue
- 7481
- Pages
- 43-49
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4031459
- OpenAlex
- W2047998066
- Cited by
- 2,254
- References
- 47
- Citations by year
- 2026: 127 · 2025: 157 · 2024: 193 · 2023: 180 · 2022: 138 · 2021: 221 · 2020: 159 · 2019: 170 · 2018: 195 · 2017: 202 · 2016: 199 · 2015: 159 · 2014: 144 · 2013: 7
- FWCI
- 792.55
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Human Genome Research Institute (HG006283, HG002385, R01HG006283, R01HG002385)
- National Institute of General Medical Sciences (R01GM040282, GM100233, R01GM100233, R01‑GM40282)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Neanderthal genome, Denisovans, Denisova Cave, Altai Mountains, inbreeding, interbreeding, gene flow, modern human ancestry, toe bone
- MeSH terms
- Africa, Animals, Female, Fossils, Gene Frequency, Heterozygote, Humans, Inbreeding, Models, Genetic, Phylogeny, Population Density, Siberia, Genome, Toe Phalanges, Gene Flow, DNA Copy Number Variations, Neanderthals, Caves
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