Research ArticleEVOLUTIONARY BIOLOGY

Neanderthal-Denisovan ancestors interbred with a distantly related hominin

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Science Advances  20 Feb 2020:
Vol. 6, no. 8, eaay5483
DOI: 10.1126/sciadv.aay5483
  • Fig. 1 A population network including four episodes of gene flow, with an embedded gene genealogy.

    Upper case letters (X, Y, N, D, and S) represent populations (Africa, Europe, Neanderthal, Denisovan, and superarchaic). Greek letters label episodes of admixture. d and xyn illustrate two nucleotide site patterns, in which 0 and 1 represent the ancestral and derived alleles. A mutation on the red branch would generate site pattern d. One on the blue branch would generate xyn. For simplicity, this figure refers to Neanderthals with a single letter. Elsewhere, we use two letters to distinguish between the Altai and Vindija Neanderthals.

  • Fig. 2 Observed site pattern frequencies.

    Horizontal axis shows the relative frequency of each site pattern in random samples consisting of a single haploid genome from each of X, Y, V, A, and D, representing Africa, Europe, Vindija Neanderthal, Altai Neanderthal, Denisovan, and superarchaic. Horizontal lines (which look like dots) are 95% confidence intervals estimated by a moving blocks bootstrap (35). Data: Simons Genome Diversity Project (SGDP) (14) and Max Planck Institute for Evolutionary Anthropology (11).

  • Fig. 3 Residuals from models α and αβγδ.

    Key: red asterisks, real data; blue circles, 50 bootstrap replicates.

  • Fig. 4 Model-averaged parameter estimates with 95% confidence intervals estimated by moving blocks bootstrap (35).

    Key: mα, fraction of Y introgressed from N; mβ, fraction of D introgressed from S; mγ, fraction of N introgressed from XY; mδ, fraction of ND introgressed from S; TXYNDS, superarchaic separation time; TXY, separation time of X and Y; TND, separation time of N and D; TN0, end of early epoch of Neanderthal history; TA, age of Altai Neanderthal fossil; TV, age of Vindija Neanderthal fossil; TD, age of Denisovan fossil; NS, size of superarchaic population; NXYND, size of populations XYND and XYNDS; NXY, size of population XY; NND, size of population ND; NN0, size of early Neanderthal population; NN1, size of late Neanderthal population. Parameters that exist in only one model are not averaged.

  • Table 1 bepe values and booma weights.

    ModelbepeWeight
    α1:16 × 10−60
    αδ0:87 × 10−60
    αγ0:62 × 10−60
    αγδ0:44 × 10−60
    αβ0:18 × 10−60
    αβγ0:17 × 10−60
    αβδ0:15 × 10−60.16
    αβγδ0:13 × 10−60.84
  • Table 2 Effect on singleton site pattern frequencies of gene flow (mδ) from superarchaics into neandersovans.

    Column 2 shows expected frequencies of singleton site patterns in a model in which mδ = 0, and all other parameters are as fitted under model αβγδ. In column 3, all parameters including mδ are as fitted under this model. Column 4 is obtained by subtracting column 2 from column 3. Expected site pattern frequencies were estimated using legosim with 107 iterations.

    Site patternFrequency
    mδ = 0mδ = 0.034Difference
    x0.155830.15174−0.00409
    y0.151760.14778−0.00398
    v0.049740.04942−0.00032
    a0.037950.037980.00003
    d0.160510.164440.00393

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/6/8/eaay5483/DC1

    Supplementary Materials and Methods

    Fig. S1. Heterozygosity as a function of FL value for genome SS6004468 of the SGDP (14).

    Fig. S2. Observed site pattern frequencies excluding the Vindija genome.

    Fig. S3. Associations between estimates of several pairs of parameters after second stage in analysis of model αβγδ.

    Table S1. Model-averaged parameter estimates.

    Table S2. Estimates under model α.

    Table S3. Estimates under model αβγδ with a data set that excludes the Vindija Neanderthal genome.

    References (3639)

  • Supplementary Materials

    This PDF file includes:

    • Supplementary Materials and Methods
    • Fig. S1. Heterozygosity as a function of FL value for genome SS6004468 of the SGDP (14).
    • Fig. S2. Observed site pattern frequencies excluding the Vindija genome.
    • Fig. S3. Associations between estimates of several pairs of parameters after second stage in analysis of model αβγδ.
    • Table S1. Model-averaged parameter estimates.
    • Table S2. Estimates under model α.
    • Table S3. Estimates under model αβγδ with a data set that excludes the Vindija Neanderthal genome.
    • References (3639)

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