Neanderthals and humans interbred in Europe for 5,400 years

Neanderthal genome to identify their genes among ours. When modern humans left Africa about 50,000 to 80,000 years ago and spread through Europe and Asia, they interbred with Neanderthals. The first hybrid offspring would have been, on average, a 50-50 mix of modern human and Neanderthal genes, and could then have themselves bred with modern humans, Neanderthals or other hybrids.

So what happened to the Neanderthal DNA? Today, Neanderthal genes are a few percent of the genome of people of European ancestry, a little more common in people of East Asian descent, and almost absent in people of African ancestry.



Coop and postdoctoral researchers Ivan Juric and Simon Aeschbacher devised methods to measure the degree of natural selection acting on Neanderthal DNA in the human genome. One hypothesis has been that Neanderthals quickly became genetically incompatible with modern humans, so their hybrid offspring were not "fit" in evolutionary terms - they either failed to thrive or were not fertile.

The researchers found something different. Rather than showing strong selection against a few Neanderthal genes, they found weak, but widespread selection against many Neanderthal DNA sequences that is slowly removing it from our genome.



Coop said that's consistent with a small, isolated population of Neanderthals mixing with a much larger population of modern humans. Inbreeding in small populations means that genetic variants can remain common even if they're harmful to some degree. But when they mix into a larger population, natural selection starts to act against those variants and weed them out.

"The human population size has historically been much larger, and this is important since selection is more efficient at removing deleterious variants in large populations," Juric said. "Weakly deleterious variants that could persist in Neanderthals could not persist in humans. We think that this simple explanation can account for the pattern of Neanderthal ancestry that we see today along the genome of modern humans."

Neandertal funerary practices remain at the forefront of palaeoanthropological research, generating heated debates following the revision of old data and new excavations at key sites such as La Chapelle-aux-Saints1,2, Roc de Marsal3, Saint-Césaire4 and La Ferrassie5. More generally, attention has focused on the variability of Neandertal mortuary practices to evaluate their cognitive and symbolic implications, especially as they may provide insights concerning the social systems of this fossil human group6. Neandertals are known to have buried their dead and are associated with mortuary behaviours that are often difficult to interpret in Palaeolithic contexts. The site of Krapina (Croatia) is an instructive example in this sense. Evidence for cannibalism was first proposed for this site as early as 19017 based on the fragmentation and traces of burning from a large collection of early Neandertal remains. This evidence has since been disputed by proponents of alternative explanations for the human bone modifications who argue for natural processes while others maintain that the anthropogenic manipulations are best interpreted in the context of secondary burials8. Several studies dedicated to cannibalism have proposed that securely identifying anthropogenic modifications related to this practice should incorporate evidence for the similar treatment of both faunal and human remains in the interest of extracting nutrients9,10,11. In addition to Gran Dolina (level TD6; Early Pleistocene) in Spain, which has produced the earliest undisputed evidence for cannibalism12, further examples have also been documented at several Western European Neandertal sites, including El Sidrón and Zafarraya13,14 in Spain, and Moula-Guercy and Les Pradelles15,16 in France.



Here we provide new data on the diversity of Neandertal mortuary behaviour, focusing on a small area of their known range, Northern Europe, during Marine Isotope Stage (MIS) 3 (ca. 60–30 thousand years ago), in order to identify small-scale processes during this short period that witnessed the disappearance of the Neandertals17. We present 99 new Neandertal remains recently identified among the collections from the Troisième caverne of Goyet (Belgium), some of which exhibit anthropogenic modifications, and discuss their implications.



The Troisième caverne (or “Third cave”) of Goyet, excavated in the latter half of the 19th and beginning of the 20th century, and again at the end of the 1990s18, is part of a large cave system located in the Mosan Basin (Supplementary Fig. S1). The most extensive excavations were carried out by Edouard Dupont in 1868, who described five “fauna-bearing levels” (FBL; ref. 19; Supplementary Note S1). The Troisième caverne yielded a rich archaeological sequence with Middle and Upper Palaeolithic deposits containing Mousterian, Lincombian-Ranisian-Jerzmanowician (LRJ), Aurignacian, Gravettian and Magdalenian artefacts as well as Neolithic and historic period material20,21,22,23. Whether the Mousterian material derives from a single or multiple phases of occupation is currently impossible to discern (Supplementary Note S2). Unfortunately, the excavation methods did not meet today’s standards, and it appears that the levels described by Dupont actually represent a mix of material from different periods (e.g., ref. 24).



Several human remains from different levels were published by Dupont19 and Hamy25, although only a few figure in the Catalogue of Fossil Hominids26, all of which were attributed to the Magdalenian. In 2004, we identified both a Neandertal mandible fragment and an isolated tooth among the human material recovered by Dupont from the Troisième caverne and currently housed at the Royal Belgian Institute of Natural Sciences (RBINS)27, making Goyet one of the few Northern European sites north of 50° N to have yielded MIS 3 Neandertal remains (Supplementary Note S1 and Supplementary Fig. S1).