Neanderthals Exchanged Human Genes 100,000 Years Ago



An unknown group of homo sapiens cross-bred with Neanderthals 100,000 years ago. Image: IVAN HEREDIA / CSIC

Neanderthals Exchanged Human Genes 100,000 Years Ago;   An unknown group of homo sapiens cross-bred with Neanderthals 100,000 years ago. Image: IVAN HEREDIA / CSIC.  For some time now, we’ve known for sure that Neanderthals and humans cross-bred, and that this happened following the migration of humans out of Africa into Europe where the Neanderthals occupied vast territories.

Neanderthals Exchanged Human Genes 100,000 Years Ago;   Researchers have found modern human DNA in the genome of a 100,000 years-old by Neanderthal humanoids. This suggests that humans and Neanderthals interbred about 50,000 years earlier than previously thought. The implications are staggering considering humans left Africa to settle Europe and Asia about 50-65,000 years ago. How was this possible? Researchers suggest that this gene flow comes from modern humans who left Africa even earlier — maybe the very first wave.

This is evidenced by the fact that Neanderthal is an obvious higher intelligence of the non-African people alive today have about 2% Neanderthal DNA, while sub-Saharan Africans (those whose ancestors were never to Europe) share 0% Neanderthal DNA.

This interbreeding event is thought to have first began some 65,000 years ago, and ended for sure 45,000 years ago when the Neanderthals who had called Europe their home for hundreds of thousands of years became extinct. Nobody knows for sure why, but a combination of competition with humans, maladaptation to climate change and starvation due to the extinction of large mammals likely brought this demise.

Recently, an international team of researchers published a paper in Nature in which they detail the genome analysis of a Neanderthal and a Siberian Denisovan, as well as the sequences of chromosome 21 of a Neanderthal found in the ‘Sidrón’ cave in Asturias, Northern Spain, and of another from Vindija, Croatia. They found that the Neanderthal genome from Siberia has sequences resembling those in humans.

The remains of the Neanderthal were found in a cave in the Altai Mountains in southern Siberia, near the Russia-Mongolia border. The other two Neanderthals, as well as the Siberian Denisovan, did not carry these modern human genes.

Dorsal Neanderthal bone found in a cave in the Altai Mountains in southern Siberia. (c) Bence Viola

Neanderthals Exchanged Human Genes 100,000 Years Ago;   Dorsal Neanderthal bone found in a cave in the Altai Mountains in southern Siberia. (c) Bence Viola. “This is the first genetic evidence of modern humans outside of Africa already 100,000 years ago. In addition, they met Neandertals around that time. So, we are pushing back about 50,000 years the time that modern humans and Neandertals met outside Africa,” co-author Sergi Castellano of the Max Planck Institute for Evolutionary Anthropology told ZME Science.

The modern human DNA sequences in the Altai Neanderthal appear to derive from a modern human group that separated early from other humans, “about the time present-day African populations diverged from one another, around 200,000 years ago,” says co-author Ilan Gronau, who is now at the Herzliya Interdisciplinary Center, Israel.

Scenario of interbreeding between modern humans and Neanderthals: Neanderthal DNA in present-day humans outside Africa originates from interbreeding that occurred 47,000 - 65,000 years ago (green arrow). Modern human DNA in Neanderthals is likely a consequence of earlier contact between the two groups roughly 100,000 years ago (red arrow). Image: Ilan Gronau

Neanderthals Exchanged Human Genes 100,000 Years Ago;   Scenario of interbreeding between modern humans and Neanderthals: Neanderthal DNA in present-day humans outside Africa originates from interbreeding that occurred 47,000 – 65,000 years ago (green arrow). Modern human DNA in Neanderthals is likely a consequence of earlier contact between the two groups roughly 100,000 years ago (red arrow).

Neanderthals Exchanged Human Genes 100,000 Years Ago;   Without a doubt, these findings will have profound implications on the evolutionary model anthropologists use to explain how we humans got to where we are today. For some time, there has been reason to believe there had been an earlier migration out of Africa judging from archaeological findings like those found at Skhul and Qafzeh in Israel.

In 2014, scientists found early homo sapiens teeth dated from 100,000 years ago in what is today China. “These fellows were taller and stronger than us. And they retained primitive features in mandibles and teeth,” Antonio Rosas from the Spanish Natural Science Museum told ZME Science.

The accepted view that humans evolved in Africa 200,000 years ago and migrated 65,000 years ago only is starting to crumble. Earlier migration waves, maybe a couple, made their way to Europe and Asia. Some went extinct, others interbred.


Genome sequence of a 45,000-year-old modern human from western Siberia:
Neanderthals Exchanged Human Genes 100,000 Years Ago;

Nature
514,
445–449
(23 October 2014)
doi:10.1038/nature13810
Received
15 May 2014
Accepted
29 August 2014
Published online
22 October 2014

Abstract

Neanderthals Exchanged Human Genes 100,000 Years Ago;   We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.

At a glance

Figures

left

  1. Geographic location, morphology and dating.
    Figure 1
  2. Principal Components (PC) analysis exploring the relationship of Ust/
    Figure 2
  3. Statistics testing whether the Ust/
    Figure 3
  4. Inferred population size changes over time.
    Figure 4
  5. Regions of Neanderthal ancestry on chromosome 12 in the Ust/
    Figure 5
  6. Dating the Neandertal admixture in Ust/
    Figure 6

right

Accession codes

Primary accessions

European Nucleotide Archive

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Neanderthals Exchanged Human Genes 100,000 Years Ago;  

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Author information

Affiliations:
Neanderthals Exchanged Human Genes 100,000 Years Ago;

  1. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China

    • Qiaomei Fu
  2. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany

    • Qiaomei Fu,
    • Ayinuer Aximu-Petri,
    • Kay Prüfer,
    • Cesare de Filippo,
    • Matthias Meyer,
    • Michael Lachmann,
    • Janet Kelso,
    • T. Bence Viola &
    • Svante Pääbo
  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Heng Li,
    • Priya Moorjani &
    • David Reich
  4. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Heng Li &
    • David Reich
  5. Department of Biological Sciences, Columbia University, New York, New York 10027, USA

    • Priya Moorjani
  6. Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA

    • Flora Jay &
    • Montgomery Slatkin
  7. Institute for Problems of the Development of the North, Siberian Branch of the Russian Academy of Sciences, Tyumen 625026, Russia

    • Sergey M. Slepchenko &
    • Dmitry I. Razhev
  8. Expert Criminalistics Center, Omsk Division of the Ministry of Internal Affairs, Omsk 644007, Russia

    • Aleksei A. Bondarev
  9. Department of Biology, Emory University, Atlanta, Georgia 30322, USA

    • Philip L. F. Johnson
  10. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany

    • Nicolas Zwyns,
    • Domingo C. Salazar-García,
    • Michael P. Richards,
    • Jean-Jacques Hublin &
    • T. Bence Viola
  11. Department of Anthropology, University of California, Davis, California 95616, USA

    • Nicolas Zwyns
  12. Department of Archaeology, University of Cape Town, Cape Town 7701, South Africa

    • Domingo C. Salazar-García
  13. Departament de Prehistòria i Arqueologia, Universitat de València, Valencia 46010, Spain

    • Domingo C. Salazar-García
  14. Research Group on Plant Foods in Hominin Dietary Ecology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany

    • Domingo C. Salazar-García
  15. Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia

    • Yaroslav V. Kuzmin &
    • Susan G. Keates
  16. Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg 620144, Russia

    • Pavel A. Kosintsev
  17. Laboratory of Archaeology, Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada

    • Michael P. Richards
  18. Siberian Cultural Center, Omsk 644010, Russia

    • Nikolai V. Peristov
  19. Santa Fe Institute, Santa Fe, New Mexico 87501, USA

    • Michael Lachmann
  20. Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK

    • Katerina Douka &
    • Thomas F. G. Higham
  21. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • David Reich

Contributions

Q.F., S.M.S., A.A.B., Y.V.K., J.K., T.B.V. and S.P. designed the research. A.A.P. and Q.F. performed the experiments; Q.F., H.L., P.M., F.J., P.L.F.J., K.P., C.d.F., M.M., M.L., M.S., D.R., J.K. and S.P. analysed genetic data; K.D. and T.F.G.H. performed 14C dating; D.C.S.-G. and M.P.R. analysed stable isotope data; N.V.P., P.A.K. and D.I.R. contributed samples and data; S.M.S., A.A.B., N.Z., Y.V.K., S.G.K., J.-J.H. and T.B.V. analysed archaeological and anthropological data; Q.F., J.K., T.B.V. and S.P. wrote and edited the manuscript with input from all authors.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

All sequence data have been submitted to the European Nucleotide Archive (ENA) and are available under the following Ust’-Ishim accession number: PRJEB6622. The data from the 25 present-day human genomes are available from (http://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project/) and from (http://cdna.eva.mpg.de/neandertal/altai/).

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