A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia.
Journal
Nature ecology & evolution
ISSN: 2397-334X
Titre abrégé: Nat Ecol Evol
Pays: England
ID NLM: 101698577
Informations de publication
Date de publication:
06 2021
06 2021
Historique:
received:
05
02
2021
accepted:
12
03
2021
pubmed:
9
4
2021
medline:
12
6
2021
entrez:
8
4
2021
Statut:
ppublish
Résumé
Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2-3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000-5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust'-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa.
Identifiants
pubmed: 33828249
doi: 10.1038/s41559-021-01443-x
pii: 10.1038/s41559-021-01443-x
pmc: PMC8175239
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
820-825Commentaires et corrections
Type : CommentIn
Références
Hublin, J.-J. et al. Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria. Nature 581, 299–302 (2020).
pubmed: 32433609
doi: 10.1038/s41586-020-2259-z
Benazzi, S. et al. Early dispersal of modern humans in Europe and implications for Neanderthal behaviour. Nature 479, 525–528 (2011).
pubmed: 22048311
doi: 10.1038/nature10617
Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).
pubmed: 25341783
pmcid: 4753769
doi: 10.1038/nature13810
Yang, M. A. et al. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Curr. Biol. 27, 3202–3208.e9 (2017).
pubmed: 29033327
pmcid: 6592271
doi: 10.1016/j.cub.2017.09.030
Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).
pubmed: 26098372
pmcid: 4537386
doi: 10.1038/nature14558
Prošek, F. et al. The excavation of the ‘Zlatý kůň’ cave in Bohemia. The report for the 1st research period of 1951 (part 2) [in Czech]. Československý kras. 5, 161–179 (1952).
Vlček, E. The Pleistocene man from the Zlatý kůň cave near Koněprusy [in Czech]. Anthropozoikum 6, 283–311 (1957).
Prošek, F. The research in the Golden Horse Cave near Koněprusy [in Czech]. Archeologické Rozhl. 4, 206–209 (1952).
Vlček, E. in Catalogue of Fossil Hominids. Part II: Europe (eds. Oakley, K. et al.) 47–64 (British Museum (Natural History), 1971).
Vlček, E. Other findings of the Pleistocene man’s remains on Zlatý kůň near Koněprusy [in Czech]. Archeologické Rozhl. 9, 305–310 (1957).
Diedrich, C. G. & Zak, K. Prey deposits and den sites of the Upper Pleistocene hyena Crocuta crocuta spelaea (Goldfuss, 1823) in horizontal and vertical caves of the Bohemian Karst (Czech Republic). Bull. Geosci. 81, 237–276 (2006).
doi: 10.3140/bull.geosci.2006.04.237
Svoboda, J. A., van der Plicht, J. & Kuželka, V. Upper Palaeolithic and Mesolithic human fossils from Moravia and Bohemia (Czech Republic): some new
doi: 10.1017/S0003598X00091754
Rmoutilová, R. et al. Virtual reconstruction of the Upper Palaeolithic skull from Zlatý kůň, Czech Republic: sex assessment and morphological affinity. PLoS ONE 13, e0201431 (2018).
pubmed: 30161127
pmcid: 6116938
doi: 10.1371/journal.pone.0201431
Brock, F., Higham, T., Ditchfield, P. & Ramsey, C. B. Current pretreatment methods for AMS radiocarbon dating at the Oxford Radiocarbon Accelerator Unit (ORAU). Radiocarbon 52, 103–112 (2010).
doi: 10.1017/S0033822200045069
Deviese, T., Comeskey, D., McCullagh, J., Ramsey, C. B. & Higham, T. New protocol for compound-specific radiocarbon analysis of archaeological bones. Rapid Commun. Mass Spectrom. 32, 373–379 (2018).
pubmed: 29247560
doi: 10.1002/rcm.8047
Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).
pubmed: 26595274
pmcid: 4918750
doi: 10.1038/nature16152
Nakatsuka, N. et al. ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium. Genome Biol. 21, 199 (2020).
pubmed: 32778142
pmcid: 7418405
doi: 10.1186/s13059-020-02111-2
Peyrégne, S. & Peter, B. M. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol. 21, 246 (2020).
pubmed: 32933569
pmcid: 7490890
doi: 10.1186/s13059-020-02123-y
Verdugo, M. P. et al. Ancient cattle genomics, origins, and rapid turnover in the fertile crescent. Science 365, 173–176 (2019).
pubmed: 31296769
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
pubmed: 22960212
pmcid: 3522152
doi: 10.1534/genetics.112.145037
Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).
pubmed: 25230663
pmcid: 4170574
doi: 10.1038/nature13673
Feldman, M. et al. Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. Nat. Commun. 10, 1218 (2019).
pubmed: 30890703
pmcid: 6425003
doi: 10.1038/s41467-019-09209-7
Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016).
pubmed: 27459054
pmcid: 5003663
doi: 10.1038/nature19310
Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).
pubmed: 27135931
pmcid: 4943878
doi: 10.1038/nature17993
Sikora, M. et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358, 659–662 (2017).
pubmed: 28982795
doi: 10.1126/science.aao1807
Seguin-Orlando, A. et al. Genomic structure in Europeans dating back at least 36,200 years. Science 346, 1113–1118 (2014).
pubmed: 25378462
doi: 10.1126/science.aaa0114
Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).
pubmed: 20448178
pmcid: 5100745
doi: 10.1126/science.1188021
Prüfer, K. et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358, 655–658 (2017).
pubmed: 28982794
pmcid: 6185897
doi: 10.1126/science.aao1887
Vernot, B. et al. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science 352, 235–239 (2016).
pubmed: 26989198
pmcid: 6743480
doi: 10.1126/science.aad9416
Hinch, A. G. et al. The landscape of recombination in African Americans. Nature 476, 170–175 (2011).
pubmed: 21775986
pmcid: 3154982
doi: 10.1038/nature10336
Kong, A. et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467, 1099–1103 (2010).
pubmed: 20981099
doi: 10.1038/nature09525
Peter, B. M. 100,000 years of gene flow between Neandertals and Denisovans in the Altai mountains. Preprint at bioRxiv https://doi.org/10.1101/2020.03.13.990523 (2020).
Moorjani, P. et al. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proc. Natl Acad. Sci. USA 113, 5652–5657 (2016).
pubmed: 27140627
doi: 10.1073/pnas.1514696113
pmcid: 4878468
Hajdinjak, M. et al. Reconstructing the genetic history of late Neanderthals. Nature 555, 652–656 (2018).
pubmed: 29562232
pmcid: 6485383
doi: 10.1038/nature26151
Black, B. A., Neely, R. R. & Manga, M. Campanian Ignimbrite volcanism, climate, and the final decline of the Neanderthals. Geology 43, 411–414 (2015).
doi: 10.1130/G36514.1
Giaccio, B., Hajdas, I., Isaia, R., Deino, A. & Nomade, S. High-precision
pubmed: 28383570
pmcid: 5382912
doi: 10.1038/srep45940
Hajdinjak, M. et al. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature https://doi.org/10.1038/s41586-021-03335-3 (2021).
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).
pubmed: 24019490
doi: 10.1073/pnas.1314445110
pmcid: 3785785
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B Biol. Sci. 370, 20130624 (2015).
doi: 10.1098/rstb.2013.0624
Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).
pubmed: 22021376
doi: 10.1093/nar/gkr771
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010).
pubmed: 20516186
doi: 10.1101/pdb.prot5448
Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protoc. 15, 2279–2300 (2020).
pubmed: 32612278
doi: 10.1038/s41596-020-0338-0
Peltzer, A. et al. EAGER: efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).
pubmed: 27036623
pmcid: 4815194
doi: 10.1186/s13059-016-0918-z
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
pubmed: 19451168
pmcid: 2705234
doi: 10.1093/bioinformatics/btp324
Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).
pubmed: 17715061
doi: 10.1073/pnas.0704665104
pmcid: 1976210
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
pubmed: 23613487
pmcid: 3694634
doi: 10.1093/bioinformatics/btt193
QGIS v.3.12 (QGIS, accessed 21 February 2020); https://qgis.org/en/site/
Natural Earth vector map data (Natural Earth, accessed 16 March 2020); https://www.naturalearthdata.com/downloads/
Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).
doi: 10.1017/S0033822200033865
Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757 (2020).
doi: 10.1017/RDC.2020.41