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, 114 (37), 9859-9863

Early History of Neanderthals and Denisovans

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Early History of Neanderthals and Denisovans

Alan R Rogers et al. Proc Natl Acad Sci U S A.

Abstract

Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal-Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

Keywords: Denisovans; Neanderthals; archaic admixture; human evolution; introgression.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
(A) Population tree representing an African population, X; a Eurasian population, Y; Neanderthals, N; and Denisovans, D. The model involves admixture, mN; time parameters, Ti; and population sizes, Ni. (B) Population tree with embedded gene tree. A mutation on the solid red branch would generate site pattern yn (shown in red at the base of the tree). One on the solid blue branch would generate ynd. Mutations on the dashed black branches would be ignored. “0” and “1” represent the ancestral and derived alleles.
Fig. 2.
Fig. 2.
(A) Open circles show relative frequencies (horizontal axis) of nucleotide sites exhibiting each site pattern (vertical axis) in four populations: X, YRI; Y, CEU; N, Neanderthal; and D, Denisovan. (B) Expanded view of four site-pattern frequencies, showing 95% confidence intervals, estimated by moving-blocks bootstrap, with 1,000 polymorphic nucleotide sites per block (13).
Fig. 3.
Fig. 3.
Covariation of estimates of mN and 2NN across bootstrap replicates. Data are as in Fig. 2.
Fig. S1.
Fig. S1.
Scatter-plot matrix showing associations among pairs of parameters. Each point represents a bootstrap replicate in the YRI.CEU data from Fig. 2A.
Fig. 4.
Fig. 4.
Estimates of Neanderthal admixture (mN) and the Neanderthal–Denisovan separation time (TND). The vertical line (Lower) shows TXYND. Horizontal lines show 95% confidence intervals based on 50 moving-blocks bootstrap replicates. All point estimates and confidence intervals are based on stage 2 of the analysis.
Fig. S3.
Fig. S3.
History of effective size of Neanderthals (solid red lines), moderns (dashed blue lines), and their ancestors, based on estimates in Figs. 4 and 5 for the YRI.CEU analysis.
Fig. 5.
Fig. 5.
Population size estimates. All point estimates are based on stage 2 of the analysis. Confidence interval for 2NXYND is based on stage 2; other intervals are based on stage 1.
Fig. 6.
Fig. 6.
Marginal sampling distributions of legofit estimates, based on 50 simulated datasets. Simulation parameters (shown as red crosses) equal the estimates from the YRI.CEU analysis in Figs. 4 and 5.
Fig. 7.
Fig. 7.
Poor fit of two constrained models. Horizontal axis shows deviation of fitted from observed site-pattern frequencies under two constraints: 2NND=10,000 (blue circles) and TND=17,318 generations (red crosses). Horizontal bars show 95% confidence intervals. Both analyses use the YRI.CEU data.
Fig. S2.
Fig. S2.
How estimates respond to various modifications of the base model. Key: base, model in Fig. 1A; DtoX, gene flow from Denisovans into Africans; HtoD, gene flow from hyperarchaics into Denisovans; NtoD, gene flow from Neanderthals to Denisovans; XYtoN, gene flow from early moderns into Neanderthals. All estimates are based on the YRI.CEU dataset.

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