Humans Interbred Neanderthals, Denisovans; mysterious species

Humans Interbred Neanderthals, Denisovans; mysterious species –  A new genome analysis study suggests that interbreeding between modern humans, Neanderthals, Denisovans and a mysterious archaic population was way more common than previously believed.

A Lord of the Rings world

denisovan

Humans Interbred Neanderthals, Denisovans; mysterious species –  An excavation in Denisova cave in Siberia, Russia, where remains of Denisovan hominins were first discovered.  Several decades ago, many anthropologists believed that humans, Neanderthals and Denisovans didn’t interbreed at all; as time passed, some evidence of this started popping out, and science acknowledged it, but still labeled it as an exception – something that happens very rarely. However, new New genome sequences from two extinct human relatives suggest that this interbreeding took place way more often.

The research team from the Royal Society in London presented their results on 18 November, suggesting that the interbreeding took place not only with Neanderthals and Denisovans, but also with another, yet to be identified group.

“What it begins to suggest is that we’re looking at a ‘Lord of the Rings’-type world — that there were many hominid populations,” says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

Neanderthals and Denisovans

Reconstruction of a Neanderthal. Photo credit: erix!

Reconstruction of a Neanderthal. Photo

Humans Interbred Neanderthals, Denisovans; mysterious species –  Neanderthals are closely related to modern humans, differing in DNA by only 0.3%, just twice the variability across contemporary humans. The first humans with proto-Neanderthal traits are believed to have existed in Europe as early as 600,000–350,000 years ago.

Meanwhile, Denisovans lived closer to the present day. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia – a cave which was also inhabited by humans and Neanderthals.

Reconstruction of a Denisovan. Photo credit.

Reconstruction of a Denisovan.

Humans Interbred Neanderthals, Denisovans; mysterious species –  The first Neanderthal and Denisovan genome sequences had a huge impact, practically revolutionizing the study of ancient human history, mostly because they showed (pretty much beyond the shadow of a doubt) that these groups interbred with anatomically modern humans, contributing to the genetic diversity of many people alive today.

Humans Interbred Neanderthals, Denisovans; mysterious species –  However, these first analyze genomes were low quality, riddled with errors and full of gaps – with better samples, studies such as this one can reach even more remarkable conclusions. David Reich, an evolutionary geneticist at Harvard Medical School in Boston, Massachusetts, led a team which developed the most complete versions of the Denisovan and Neanderthal genomes — matching the quality of contemporary human genomes.

A new population?

So after the news that interbreeding was rather common, everyone was puzzled about this (genetically) new species – what could it be? Apparently, anthropologists are just as puzzled as us.

“We don’t have the faintest idea,” says Chris Stringer, a paleoanthropologist at the London Natural History Museum, who was not involved in the work. He speculates that the population could be related to Homo heidelbergensis, a species that left Africa around half a million years ago and later gave rise to Neanderthals in Europe. “Perhaps it lived on in Asia as well,” Stringer says.


Genome sequence of a 45,000-year-old modern human from western Siberia:
Humans Interbred Neanderthals, Denisovans; mysterious species –

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

Humans Interbred Neanderthals, Denisovans; mysterious species –  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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Humans Interbred Neanderthals, Denisovans; mysterious species – 

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Author information

Affiliations:
Humans Interbred Neanderthals, Denisovans; mysterious species –

  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:
Humans Interbred Neanderthals, Denisovans; mysterious species –

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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