Neanderthals and humans interbred in Europe for 5,400 years

Fig. 1.
(A) Neighbor-joining tree based on the number of pairwise differences between individuals. Phenotypic categories enriched in amino acid-changing substitutions on the lines to Neandertals and to modern humans, respectively, are indicated. The bar indicates 50 inferred substitutions per megabase. (B) Neighbor-joining tree of pairwise FST values for the same individuals. The bar indicates an FST of 0.05.

To investigate the extent to which the population history reflected in the low genetic diversity affected the evolution of coding regions, we investigated derived alleles present in Neandertals and compared them with those of the present-day Africans, Europeans, and Asians (Table 2). We found that the fraction of all derived SNPs inferred to change amino acids in Neandertals (51.1%) is larger than that in Africans (45.7%; P = 3.1 × 10−11; G-test), Europeans (46.4%; P = 6.9 × 10−10), and Asians (46.7%; P = 4.5 × 10−7) (Table 2). We used PolyPhen-2 (16) to assess whether the amino acid-changing SNPs in Neandertals are enriched in alleles inferred to affect protein function or structure and thus likely to be slightly deleterious. The proportion of such SNPs in the Neandertals (45.4%) is larger than that in Africans (36.4%; G-test; P = 1.6 × 10−14), Europeans (37.9%; P = 4.5 × 10−9), and Asians (38.1%; P = 1.3 × 10−9) (Table 2). Similarly, the proportion of such SNPs in conserved protein sites [PhastCons (17)] is larger in the Neandertals (50.1%) than in the Africans (38.1%; G-test; P < 10−20), Europeans (40.2%; P = 1.1 × 10−15), and Asians (39.7%; P < 10−20) (Table 2). Furthermore, a physicochemical classification of amino acid substitutions, the Grantham score (GS) (18), shows that the proportion of derived SNPs in the Neandertals that cause radical (GS >100) amino acid changes is larger than that in present-day humans (Table 2). Derived alleles in conserved protein sites that are homozygous in all individuals analyzed also are more frequent in Neandertals (39.6%) than in Africans (G-test; 29.4%; P = 2.1 × 10−3), Europeans (27.8%; P = 1.6 × 10−5), and Asians (26.9%; P = 5.9 × 10−6) (Table 2).

Although only six Neandertal chromosomes are available, we note that among derived amino acid-changing alleles likely to have been at low frequency in Neandertals because they are seen once among the six chromosomes (Fig. 2), a higher proportion is inferred to alter protein structure or function in Neandertals (49.1% by PolyPhen-2; similar results with PhastCons) than in Africans (G-test; 38.3%; P = 2.2 × 10−12), Europeans (40.6%; P = 8.8 × 10−7), and Asians (41.8%; P = 5.1 × 10−6). Furthermore, we note that these low-frequency, putatively deleterious alleles have a stronger inferred impact on proteins in Neandertals than in Africans (P < 2.2 × 10−16), Europeans (P = 6.7 × 10−9), or Asians (P = 2.0 × 10−7) (Fig. 2 and SI Appendix).


Fig. 2.
Frequency spectra of nonsynonymous derived alleles classified by PolyPhen-2 as either benign or deleterious in Neandertals and present-day humans. The ratio of deleterious to benign derived alleles is higher in Neandertals than in the present-day humans. See Table S19 for the actual allele counts and Fig. S10 for the frequency spectra of nonsynonymous derived alleles assessed by PhastCons and GS.

We conclude that the patterns of coding variation in Neandertals differ strongly from those in present-day humans, a fact likely to be the result of differences in their demographic histories. Inferences from the complete Neandertal genome suggest that sometime after 0.5–1.0 Mya, the ancestral Neandertal population decreased in size, whereas the ancestors of present-day humans increased in number (10). A low population size over a long time would reduce the efficacy of purifying selection and contribute to a larger fraction of slightly deleterious alleles, particularly at low frequency, but not necessarily to the absolute number of slightly deleterious alleles per individual (19) (SI Appendix). The fact that the three Neandertals carry longer tracts of homozygosity and differ more from one another than present-day humans within continents further suggests that Neandertals may have been subdivided in small local populations. However, we note that the three Neandertal individuals analyzed are not contemporaneous but differ in time by perhaps as much as 20,000 y. It therefore is crucial for DNA sequences from more Neandertals to be generated when suitable specimens become available. It is also crucial for more complex demographic scenarios, for example involving recurrent population reductions and expansions, to be explored to fully understand the differences in population history between Neandertals and modern humans.

In the Neandertal lineage after the split from Denisovans, only the phenotype category “hyperlordosis” is overrepresented (Fig. 1A; binomial test; P = 4.5 × 10−5; FDR = 2.1 × 10−2). This is interesting because Neandertals had a reduced lordotic curvature relative to other archaic hominins as well as to modern humans (21). Changes in the six genes associated with this phenotype (CUL7, GLB1, NEB, COL2A1, HSPG2, and VPS13B) thus may have contributed to this feature of the Neandertal morphology.

PNAS May 6, 2014 vol. 111 no. 18 6666-6671

Using several different methods of DNA analysis, an international research team has identified an interbreeding event between Neanderthals and modern humans that occurred an estimated 100,000 years ago, which is tens of thousands of years earlier than other such events previously documented. They suggest that some modern humans left Africa early and mixed with Neanderthals. These modern humans later became extinct and are therefore not among the ancestors of present-day people outside Africa who left Africa about 65,000 years ago.

The team’s evidence of “gene flow” from descendants of modern humans into the Neanderthal genome applies to one specific Neanderthal, whose remains were found in a cave in the Altai Mountains in southern Siberia, near the Russia-Mongolia border. Two Neanderthals from European caves that were sequenced for this study — one from Croatia, another from Spain — both lack DNA derived from modern humans. The team also analyzed the genome of another extinct human, a Denisovan, whose remains were found in the same cave in the Altai Mountains as the Neanderthal bone. Unlike the Neanderthal individual, the Denisovan individual did not carry any modern human DNA. That does not mean modern humans never mated with Denisovans or European Neanderthals. What it does mean, Siepel clarifies, is that “the signal we are seeing in the Altai Neanderthal probably comes from an interbreeding event that occurred after this Neanderthal lineage diverged from its European cousins, a little more than 100,000 years ago.”



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,” adds Gronau, co-first author of this work.

The modern human who contributed genes to this particular Neanderthal individual must have come from a population that left Africa long before the migration of the ancestors of present-day Europeans and Asians from Africa less than 65,000 years ago, the scientists say. Thus, there must have been a long lag between when this group branched off the modern human family tree, roughly 200,000 years ago, and when they left their genetic mark in the Altai Neanderthal, about 100,000 years ago, before themselves being lost to extinction.