Interbreeding between Neanderthals and modern humans

What we know now

A topic of perennial interest to scholars and lay people alike is did Neanderthals and modern humans interbreed? Until recently, there was no strong evidence one way or another, although there was no reason to suppose that they did not. While Neanderthals would certainly have appeared strange to modern humans and vice versa, they would not necessarily have seemed unattractive to each other. For a present-day human, having sex with a Neanderthal could be a somewhat hazardous affair, given the considerably superior physical strength of the latter. To the rather more powerfully-built Homo sapiens of that era, it might have been less of an issue. There is no reason to suppose that such a union would not have led to viable and probably fertile offspring, as is often the case among closely-related species.

However, prior to 2010, there was no definite evidence for or against interbreeding. No convincing fossil evidence of a Neanderthal/modern hybrid has ever come to light, suggesting that interbreeding was rare. Claims that the 24,500-year-old skeleton of a 4-year-old child found at Abrigo do Lagar Velho, Portugal in 1998 is an example of a hybrid 1 have not been widely accepted. Notably, the burial was typical of the Gravettian, a culture that is firmly associated with modern humans. It is possible that the infant was simply an unusually stocky modern human juvenile, or a ‘chunky child’ as one critic put it 2. Recently, it been claimed that a Neanderthal lower jawbone from Riparo Mezzena, northern Italy, shows some modern traits, including an incipient chin that might have arisen from interbreeding with modern humans 3, possibly living at the nearby site of Grotta di Fumane 4. It is too early yet to say whether or not this claim will become widely accepted.

Nevertheless, Erik Trinkaus 5 claimed there was evidence to show that Neanderthals and modern humans did interbreed up to Gravettian times. Trinkaus compared remains of early European modern humans with early modern humans from Africa. He claimed that the European fossils exhibit a number of distinctive Neanderthal traits, but that these features were not present among the African samples. This, Trinkaus believes, is best explained by the assimilation of some Neanderthals into early modern human populations as the latter dispersed westwards across Europe.

In the absence of unequivocal fossil evidence, researchers turned to genetics. Initially, the evidence was negative. Studies of mitochondrial DNA samples obtained from Neanderthal and contemporary modern human remains in Europe found no evidence for interbreeding between the two 6,7,8. Computer simulations of modern human migration into Europe suggested that any interbreeding must have been minimal; or otherwise the modern genome would have become progressively diluted by that of Neanderthals as the modern populations moved westwards. By the time the migrants reached the northwestern corner of Europe, they would have been close to 100 percent Neanderthal 9.

However, over the next three years, tentative genetic evidence began to emerge for interbreeding between modern and archaic humans. Researchers investigated genetic sequence data from Europeans, East Asians and West Africans and found traces of an archaic contribution to the modern genome. No particular archaic species could be identified, but a Neanderthal contribution, at least to the European genome, seemed likely 10,11. This conclusion was soon vindicated. A project to sequence the Neanderthal genome was commenced in 2006 at the Max Planck Institute for Evolutionary Anthropology 12,13, and in May 2010, researchers published a first draft of the Neanderthal genome 14.

With the initial announcement came the dramatic news that made headlines around the world. It turned out that between one and four percent of the genome of modern non-Africans was derived from Neanderthals. In other words, the answer to the million dollar question was ‘yes, they did interbreed – but not in Africa’. The researchers compared the Neanderthal genome with those of five present-day individuals: two indigenous Africans (one San from South Africa and one Yoruba from West Africa) and three Eurasians (one from Papua New Guinea, one from China and one from France). The results showed that Neanderthals were more closely related to non-Africans than to Africans. This is not particularly surprising, as Neanderthals are not known to have lived in Africa. Any interbreeding has generally been supposed to have occurred within the known range of the Neanderthals, in Europe and western Asia. What was unexpected was that no difference was found between Papua New Guinean, Chinese and French individuals in terms of their degree of relatedness to Neanderthals.

However, the authors of the Max Planck report could not rule out the possibility that their results reflected substructure in the early modern human population of Africa rather than interbreeding; in other words the splitting of the population into smaller sub-populations that were isolated from one another by barriers such as mountain ranges, rivers, or the appearance of deserts during periods of low rainfall. It was suggested that such conditions might have existed in Africa after Neanderthals diverged from modern humans, leaving some groups more closely related to Neanderthals than others. If members one of these were the ancestors of present-day non-Africans, then this would also be consistent with the genetic findings.

Although the Max Planck group felt that this scenario was less likely than the interbreeding hypothesis, independent researchers later claimed that the substructure model is a more realistic scenario. They used a mathematical model to represent a connected string of regional populations spanning Africa and Eurasia. After the string split, the Eurasian and African parts of the range subsequently evolved into Neanderthals and modern humans respectively. For the latter, groups geographically closest to the split (i.e. in North Africa) remained more closely related to Neanderthals than those further south 15.

Assuming that Neanderthals and modern humans did interbreed, the implication was that it must have happened at a time before the ancestors of the present-day Asian, Australasian and European populations diverged from one another – presumably soon after modern humans first left Africa, and long before they reached Europe. If the population that left Africa was small, only limited interbreeding would be necessary to leave the Neanderthal contribution fixed in the modern non-African genome for all time, as numbers increased during the subsequent peopling of the world. Conversely, later encounters, for example in Europe, would leave little genetic trace. Modern populations were by that time large in comparison to Neanderthal groups.

Subsequent work by independent researchers initially appeared to back this conclusion 16, and it was suggested that the interbreeding had occurred in Southwest Asia from 47,000 to 65,000 years ago 17. Researchers also demonstrated that the substructure model was unlikely to explain genetic similarities between Neanderthals and modern non-African populations 17,18.

However, later reports found that non-Africans were not, after all, equally related to Neanderthals, and that there are higher levels of Neanderthal ancestry in East Asians than in Europeans 19,20,21. Given that Neanderthals lived in Europe but are not known from East Asia, this was an unexpected development. It was also reported that North Africans do carry a Neanderthal genetic signature 22,20, although this is less mysterious as it is believed that some modern pre-Neolithic people later migrated back to Africa from Southwest Asia 23,24.

One interpretation of the East Asian data is that after the ancestors of present-day Europeans and East Asians had separated from one another, the latter encountered and interbred with a second, more easterly population of Neanderthals. As noted above, the latter are now known from as far to the east as the Altai Mountains, and it is possible that their range also extended further south.

On the other hand it is possible that instead of one-off events, interbreeding occurred throughout the Neanderthal range – but only very occasionally. Mathematical studies suggest that the Neanderthal component of the modern genome could be accounted for even if interbreeding only occurred once every 70 to 80 generations. Such a low rate could be due either to social factors or to limited reproductive compatibility. It would also account for the absence of a Neanderthal contribution to the modern mitochondrial gene pool, as Neanderthal mitochondrial DNA would be rapidly eliminated by genetic drift 25,26.

The differences between present-day European and East Asian populations are probably more related to differing effects of natural selection in the two regions than they are to additional episodes of interbreeding in the East. The latest research suggests that around 20 percent of the Neanderthal genome survives in the present-day population, although individuals each only possess a small fraction of this amount 21. Many useful Neanderthal genes have been incorporated into the modern genome; for example those involved with the production of keratin, a protein that is used in skin, hair and nails 27. In East Asian populations, many genes involved with protection from the sun’s UV rays are of Neanderthal origin 28. It is likely that the transfer of Neanderthal genes helped modern humans to adapt to conditions away from their African homeland

Curiously, some deleterious genes also have a Neanderthal connection, including those implicated in type 2 diabetes and in Crohn’s disease. Possibly, these genes were once advantageous, and it is only our changed diet since the advent of agriculture that has triggered these adverse effects. Significantly, Neanderthal DNA was largely absent from the X chromosome and genes associated with modern testes. The implication is that Neanderthal DNA in these regions led to reduced male fertility, or sterility 27, consistent with the view that Neanderthals and modern humans were at the limits of biological compatibility.

The non-random distribution of Neanderthal DNA in the modern genome clearly indicates that natural selection had a significant role to play, with both positive and negative selection determining Neanderthal gene frequencies. It is very likely that selective factors were at least partially responsible for the higher incidence of Neanderthal DNA in East Asian populations.

References:

1.    Duarte, C. et al., The Early Upper Paleolithic Human Skeleton from the Abrigo do Lagar Velho (Portugal) and Modern Human Emergence in Iberia. PNAS 96, 7604–7609 (1999).

2.    Tattersall, I. & Schwartz, J., Hominids and hybrids: The place of Neanderthals in human evolution. PNAS 96, 7117–7119 (1999).

3.    Condemi, S. et al., Possible Interbreeding in Late Italian Neanderthals? New Data from the Mezzena Jaw (Monti Lessini, Verona, Italy). PLoS One 8 (3) (2013).

4.    Longo, L. et al., Did Neandertals and anatomically modern humans coexist in northern Italy during the late MIS 3? Quaternary International 259, 102–112 (2012).

5.    Trinkaus, E., European early modern humans and the fate of the Neandertals. PNAS 104 (18), 7367–7372 (2007).

6.    Caramelli, D. et al., Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. PNAS 100 (11), 6593–6597 (2003).

7.    Serre, D. et al., No Evidence of Neandertal mtDNA Contribution to Early Modern Humans. PLoS Biology 2 (3), 0313-0317 (2004).

8.    Caramelli, D. et al., A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences. PLoS One 3 (7) (2008).

9.    Currat, M. & Excoffier, L., Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe. PLoS Biology 2 (12), 2264-2274 (2004).

10.  Plagnol, V. & Wall, J., Possible Ancestral Structure in Human Populations. PLoS Genetics 2 (7), 972-979 (2006).

11.  Wall, J., Lohmueller, K. & Plagnol, V., Detecting Ancient Admixture and Estimating Demographic Parameters in Multiple Human Populations. Molecular Biology and Evolution 26 (8), 1823-1827 (2009).

12.  Green, R. et al., Analysis of one million base pairs of Neanderthal DNA. Nature 444, 330-336 (2006).

13.  Green, R. et al., A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell 134, 416–426 (2008).

14.  Green, R. et al., A Draft Sequence of the Neandertal Genome. Science 328, 710-722 (2010).

15.  Eriksson, A. & Manica, A., Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. PNAS 109 (35), 13956–13960 (2012).

16.  Yotova, V. et al., An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations. Molecular Biology and Evolution 28 (7), 1957-1962 (2011).

17.  Sankararaman, S., Patterson, N., Li, H., Pääbo, S. & Reich, D., The Date of Interbreeding between Neandertals and Modern Humans. PLoS Genetics 8 (10) (2012).

18.  Yang, M., Malaspinas, A., Durand, E. & Slatkin, M., Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity. Molecular Biology and Evolution 29 (10), 2987–2995 (2012).

19.  Meyer, M. et al., A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 338, 222-226 (2012).

20.  Wall, J. et al., Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics 194, 199-209 (2013).

21.  Vernot, B. & Akey, J., Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science 343, 1017-1021 (2014).

22.  Sánchez-Quinto, F. et al., North African Populations Carry the Signature of Admixture with Neandertals. PLoS One 7 (10) (2012).

23.  Olivieri, A. et al., The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa. Science 314, 1757-1770 (2006).

24.  González, A. et al., Mitochondrial lineage M1 traces an early human backflow to Africa. BMC Genomics 8 (223) (2007).

25.  Currat, M. & Excoffier, L., Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression. PNAS 108 (37), 15129-15134 (2011).

26.  Neves, A. & Serva, M., Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans. PLoS One 7 (10) (2012).

27.  Sankararaman, S. et al., The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354–357 (2014).

28.  Ding, Q., Hu, Y., Xu, S., Wang, J. & Jin, L., Neanderthal Introgression at Chromosome 3p21.31 Was Under Positive Natural Selection in East Asians. Molecular Biology and Evolution 31 (3), 683-695 (2013).

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