The Complete Genome Sequence of a Neanderthal from the Altai Mountains

Overview

Journal Nature

Specialty Science

Date 2013 Dec 20

PMID 24352235

Citations 783

Authors

Kay Prufer

Fernando Racimo

Nick Patterson

Flora Jay

Sriram Sankararaman

Susanna Sawyer

Anja Heinze

Gabriel Renaud

Peter H Sudmant

Cesare de Filippo

Heng Li

Swapan Mallick

Michael Dannemann

Qiaomei Fu

Martin Kircher

Martin Kuhlwilm

Michael Lachmann

Matthias Meyer

Matthias Ongyerth

Michael Siebauer

Christoph Theunert

Arti Tandon

Priya Moorjani

Joseph Pickrell

James C Mullikin

Samuel H Vohr

Richard E Green

Ines Hellmann

Philip L F Johnson

Helene Blanche

Howard Cann

Jacob O Kitzman

Jay Shendure

Evan E Eichler

Ed S Lein

Trygve E Bakken

Liubov V Golovanova

Vladimir B Doronichev

Michael V Shunkov

Anatoli P Derevianko

Bence Viola

Montgomery Slatkin

David Reich

Janet Kelso

Svante Paabo

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Computational Genomics and Its Applications to Anthropological Questions.

Witt K, Villanea F Am J Biol Anthropol. 2025; 186 Suppl 78:e70010.

PMID: 40071816 PMC: 11898561. DOI: 10.1002/ajpa.70010.

Semicircular canals shed light on bottleneck events in the evolution of the Neanderthal clade.

Urciuoli A, Martinez I, Quam R, Arsuaga J, Keeling B, Diez-Valero J Nat Commun. 2025; 16(1):972.

PMID: 39979299 PMC: 11842635. DOI: 10.1038/s41467-025-56155-8.

A humanized NOVA1 splicing factor alters mouse vocal communications.

Tajima Y, Vargas C, Ito K, Wang W, Luo J, Xing J Nat Commun. 2025; 16(1):1542.

PMID: 39966351 PMC: 11836289. DOI: 10.1038/s41467-025-56579-2.

Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl.

Wang G, Zhang X, Zhao X, Ren X, Chen A, Dai W Gigascience. 2025; 14.

PMID: 39965774 PMC: 11835448. DOI: 10.1093/gigascience/giae124.

A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome.

Liang S, Ren T, Zhang J, He J, Wang X, Jiang X Genome Biol. 2025; 26(1):32.

PMID: 39962554 PMC: 11834205. DOI: 10.1186/s13059-025-03502-z.

References

Briggs A, Stenzel U, Meyer M, Krause J, Kircher M, Paabo S . Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 2009; 38(6):e87. PMC: 2847228. DOI: 10.1093/nar/gkp1163. View

Abecasis G, Auton A, Brooks L, DePristo M, Durbin R, Handsaker R . An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491(7422):56-65. PMC: 3498066. DOI: 10.1038/nature11632. View

Awadalla P, Gauthier J, Myers R, Casals F, Hamdan F, Griffing A . Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Am J Hum Genet. 2010; 87(3):316-24. PMC: 2933353. DOI: 10.1016/j.ajhg.2010.07.019. View

Meyer M, Kircher M, Gansauge M, Li H, Racimo F, Mallick S . A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012; 338(6104):222-6. PMC: 3617501. DOI: 10.1126/science.1224344. View

Kokovay E, Wang Y, Kusek G, Wurster R, Lederman P, Lowry N . VCAM1 is essential to maintain the structure of the SVZ niche and acts as an environmental sensor to regulate SVZ lineage progression. Cell Stem Cell. 2012; 11(2):220-30. DOI: 10.1016/j.stem.2012.06.016. View

Skoglund P, Jakobsson M . Archaic human ancestry in East Asia. Proc Natl Acad Sci U S A. 2011; 108(45):18301-6. PMC: 3215044. DOI: 10.1073/pnas.1108181108. View

Kitzman J, MacKenzie A, Adey A, Hiatt J, Patwardhan R, Sudmant P . Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol. 2010; 29(1):59-63. PMC: 3116788. DOI: 10.1038/nbt.1740. View

Reich D, Green R, Kircher M, Krause J, Patterson N, Durand E . Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010; 468(7327):1053-60. PMC: 4306417. DOI: 10.1038/nature09710. View

Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L . ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics. 2010; 11:116. PMC: 2848233. DOI: 10.1186/1471-2105-11-116. View

10.

Kong A, Frigge M, Masson G, Besenbacher S, Sulem P, Magnusson G . Rate of de novo mutations and the importance of father's age to disease risk. Nature. 2012; 488(7412):471-5. PMC: 3548427. DOI: 10.1038/nature11396. View

11.

Wall J, Yang M, Jay F, Kim S, Durand E, Stevison L . Higher levels of neanderthal ancestry in East Asians than in Europeans. Genetics. 2013; 194(1):199-209. PMC: 3632468. DOI: 10.1534/genetics.112.148213. View

12.

Green R, Krause J, Briggs A, Maricic T, Stenzel U, Kircher M . A draft sequence of the Neandertal genome. Science. 2010; 328(5979):710-722. PMC: 5100745. DOI: 10.1126/science.1188021. View

13.

Rios D, McLaren W, Chen Y, Birney E, Stabenau A, Flicek P . A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics. 2010; 11:238. PMC: 2882931. DOI: 10.1186/1471-2105-11-238. View

14.

Scally A, Durbin R . Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet. 2012; 13(10):745-53. DOI: 10.1038/nrg3295. View

15.

Hublin J . Out of Africa: modern human origins special feature: the origin of Neandertals. Proc Natl Acad Sci U S A. 2009; 106(38):16022-7. PMC: 2752594. DOI: 10.1073/pnas.0904119106. View

16.

Kircher M, Stenzel U, Kelso J . Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol. 2009; 10(8):R83. PMC: 2745764. DOI: 10.1186/gb-2009-10-8-r83. View

17.

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

18.

Abi-Rached L, Jobin M, Kulkarni S, McWhinnie A, Dalva K, Gragert L . The shaping of modern human immune systems by multiregional admixture with archaic humans. Science. 2011; 334(6052):89-94. PMC: 3677943. DOI: 10.1126/science.1209202. View

19.

Hofreiter M, Jaenicke V, Serre D, Von Haeseler A, Paabo S . DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001; 29(23):4793-9. PMC: 96698. DOI: 10.1093/nar/29.23.4793. View

20.

Sankararaman S, Patterson N, Li H, Paabo S, Reich D . The date of interbreeding between Neandertals and modern humans. PLoS Genet. 2012; 8(10):e1002947. PMC: 3464203. DOI: 10.1371/journal.pgen.1002947. View