Interbreeding
An alternative to extinction is that Neanderthals were absorbed into the Cro-Magnon population by interbreeding. This would be counter to strict versions of the Recent African Origin, since it would imply that at least part of the genome of Europeans would descend from Neanderthals, who left Africa at least 350,000 years ago.
The most vocal proponent of the hybridization hypothesis is Erik Trinkaus of Washington University. Trinkaus claims various fossils as hybrid individuals, including the "child of Lagar Velho", a skeleton found at Lagar Velho in Portugal dated to about 24,000 years ago. In a 2006 publication co-authored by Trinkaus, the fossils found in 1952 in the cave of Pestera Muierii, Romania, are likewise claimed as hybrids.
Genetic studies indicate some form of hybridization between archaic humans and modern humans had taken place after modern humans emerged from Africa. An estimated 1 to 4 percent of the DNA in Europeans and Asians (e.g. French, Chinese and Papua probands) is non-modern, and shared with ancient Neanderthal DNA rather than with sub-Saharan Africans (e.g. Yoruba and San probands).
Modern-human findings in Abrigo do Lagar Velho, Portugal of 24,500 years ago, allegedly featuring Neanderthal admixtures, have been published. However, the interpretation of the Portuguese specimen is disputed.
Jordan, in his work Neanderthal, points out that without some interbreeding, certain features on some "modern" skulls of Eastern European Cro-Magnon heritage are hard to explain. In another study, researchers have recently found in Peştera Muierilor, Romania, remains of European humans from 30 thousand years ago who possessed mostly diagnostic "modern" anatomical features, but also had distinct Neanderthal features not present in ancestral modern humans in Africa, including a large bulge at the back of the skull, a more prominent projection around the elbow joint, and a narrow socket at the shoulder joint. Analysis of one skeleton's shoulder showed these humans, like Neanderthal, did not have the full capability for throwing spears.
An analysis of a first draft of the Neanderthal genome by Richard E. Green et al. from Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany released in May 2010 indicates interbreeding may have occurred. "Those of us who live outside Africa carry a little Neanderthal DNA in us," said Svante Pääbo, who led the study. "The proportion of Neanderthal-inherited genetic material is about 1 to 4 percent. It is a small but very real proportion of ancestry in non-Africans today," says Dr. David Reich of Harvard Medical School in Boston, who worked on the study. This research compared the genome of the Neanderthals to five modern humans from China, France, sub-Saharan Africa, and Papua New Guinea. The finding is that about 1 to 4 percent of the genes of the non-Africans came from Neanderthals, compared to the baseline defined by the two Africans. This indicates a gene flow from Neanderthals to modern humans, i.e., interbreeding between the two populations. Since the three non-African genomes show a similar proportion of Neanderthal sequences, the interbreeding must have occurred early in the migration of modern humans out of Africa, perhaps in the Middle East. No evidence for gene flow in the direction from modern humans to Neanderthals was found. The latter result would not be unexpected if contact occurred between a small colonizing population of modern humans and a much larger resident population of Neanderthals. A very limited amount of interbreeding could explain the findings, if it occurred early enough in the colonization process.
Although modern humans share some nuclear DNA with the extinct Neanderthals, the two species do not share any mitochondrial DNA, which in primates is always maternally transmitted. This observation has prompted the hypothesis that whereas female humans interbreeding with male Neanderthals were able to generate fertile offspring, the progeny of female Neanderthals who mated with male modern humans were either rare, absent or sterile (in line with Haldane's rule).
While interbreeding is viewed as the most parsimonious interpretation of the genetic discoveries, the authors point out they cannot conclusively rule out an alternative scenario, in which the source population of non-African modern humans was already more closely related to Neanderthals than other Africans were, due to ancient genetic divisions within Africa.
Among the genes shown to differ between present-day humans and Neanderthals were RPTN, SPAG17, CAN15, TTF1 and PCD16.
Read more about this topic: Neanderthal Extinction Hypotheses