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The genome of the offspring of a Neanderthal mother and a Denisovan father - PubMed

The genome of the offspring of a Neanderthal mother and a Denisovan father

Viviane Slon et al. Nature. 2018 Sep.

Abstract

Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago1,2. Here we present the genome of 'Denisova 11', a bone fragment from Denisova Cave (Russia)3 and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave4-6. The mother came from a population more closely related to Neanderthals who lived later in Europe2,7 than to an earlier Neanderthal found in Denisova Cave8, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Extended Data Figure 1
Extended Data Figure 1. Maximum cortical thickness of femora, tibiae, humeri, radii and ulnae among humans from the Bronze Age and two Neandertals, compared to the minimum thickness of Denisova 11 (dashed line).
Extended Data Figure 2
Extended Data Figure 2. Percentage of sites at which Denisova 11 and genomes simulated under the demographic model detailed in SI 6 carry two Neandertal alleles (NN, blue), two Denisovan alleles (DD, red), or one allele of each type (ND, purple).

a. Percentages calculated for two random DNA fragments from Denisova 11 (leftmost column) and from simulated F1, F2, Neandertal (NF0) or Denisovan (DF0) genomes (columns 2-5). b. Proportions of sites for the simulated genotypes, prior to sampling two fragments.

Extended Data Figure 3
Extended Data Figure 3. Neandertal and Denisovan allele proportions from Denisova 11 in 1 Mb windows (100 kb step, n=26,414 windows).

Y-axis shows –log(p-value) of the deviation of Neandertal and Denisovan allele counts from the genome-wide average (chi-square test of goodness-of-fit; see SI 7); color shows the proportion of alleles matching the Neandertal state (%N) within each 1 Mb window.

Figure 1
Figure 1. Location of Neandertals (blue), Denisovans (red) and ancient modern humans (yellow) dated to ~40 kya or older, from which sufficient nuclear DNA fragments have been recovered to enable their attribution to a hominin group.

Full or abbreviated names of specimens are shown near each figure. Asterisks indicate that the genome was sequenced to high-coverage, a question mark that the individual is of unknown sex. Note that Oase 1 has recent Neandertal ancestry (blue dot) that is beyond the amount seen in non-Africans. Denisova 3 has also been found to carry a small percentage of Neandertal ancestry. Data taken from ,,–,–,–.

Figure 2
Figure 2. Denisova 11 carries both Neandertal and Denisovan ancestry.

a. Percentage of DNA fragments in Denisova 11 carrying derived alleles seen on each branch of a tree relating a Neandertal, a Denisovan and a present-day human genome. b. Distribution of heterozygosity per chromosome in two Neandertals (blue), a Denisovan (red), Denisova 11 (purple) and present-day humans (N=235 non-African [yellow] and N=44 African individuals [orange] from 28), and the expectation for a Neandertal-Denisovan F1 offspring (grey). The violins represent the distribution from the minimum and maximum heterozygosity values for the autosomes of each archaic hominin and of present-day humans (n=5,170 pairs of chromosomes for non-Africans and n=968 for Africans). White squares represent autosome-wide estimates for the archaic hominins, and the average of estimates across individuals for present-day humans. c. Percentage of sites at which two sampled DNA fragments both carry “Neandertal alleles” (blue), “Denisovan alleles” (red), or one allele of each type (purple); and the expectations for an offspring of a Neandertal and a Denisovan (F1), of two F1 parents (F2), and of an F1 and a Denisovan (F1xD). The expected proportions for simulated Neandertal and Denisovan genomes are shown in Extended Data Figure 2.

Figure 3
Figure 3. The distribution of Neandertal-like and Denisovan-like alleles across the Denisova 11 genome.

Positions where one randomly drawn DNA fragment matches the Neandertal genome and another matches the Denisovan genome are marked in purple. Positions are marked in blue if both DNA fragments match the Neandertal genome, and in red if both match the Denisovan genome. Black lines indicate centromeres. The inset shows one region out of five (green boxes) where both chromosomes carry predominantly Neandertal-like alleles. For comparison, the distribution of alleles in this region is shown for a Neandertal genome (Goyet Q56-1).

Figure 4
Figure 4. Relationships and gene flow events between Neandertal and Denisovan populations inferred from genome sequences.

Diamonds indicate ages of specimens estimated via branch shortening; circles indicate population split times estimated from allele sharing between Denisova 11 and the high-coverage genomes (blue and red) and among the three high-coverage genomes (yellow, from 2); the arrow indicates Neandertal gene flow into Denisovans. Markers indicate the means of these estimates, error bars indicate 95% confidence intervals (CIs) based on block jackknife resampling across the genome (n=523 blocks). Note that the CIs do not take the uncertainty with respect to population size, mutation rates or generation times into account. Ages before present are based on a human-chimpanzee divergence of 13 million years,.

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References

    1. Meyer M, et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature. 2016;531:504–507. doi: 10.1038/nature17405. - DOI - PubMed
    1. Prüfer K, et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science. 2017;358:655–658. doi: 10.1126/science.aao1887. - DOI - PMC - PubMed
    1. Brown S, et al. Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis. Scientific Reports. 2016;6:23559. doi: 10.1038/srep23559. - DOI - PMC - PubMed
    1. Krause J, et al. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature. 2010;464:894–897. doi: 10.1038/nature08976. - DOI - PMC - PubMed
    1. Reich D, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010;468:1053–1060. doi: 10.1038/nature09710. - DOI - PMC - PubMed

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