That humans today have genes from Neanderthals, Denisovans and some other ancient cousin species seems to be quite clear from the genetic evidence (though I am always quite amazed at the wondrous ability to extract DNA from ancient bones). In fact, it seems that the mainstream of AMH had various breeding encounters with these other species at many different times and (presumably) at many geographic locations. These encounters could not have been rare isolated events suggesting that there was more than a little promiscuity in the pleistocene.
Gene flow in the late pleistocene (Kay Prüfer et al)
It has been thought that most of the Neanderthal/AMH interactions must have taken place in the Middle East or central Asia, but new work indicates that these interactions took place in Europe as well. DNA analysis of a jawbone from a Romanian cave from about 40,000 years ago had a Neanderthal for a great-great- grandparent.
I take this grandparent to be a Neanderthal grandmother who was abducted by some marauding group of promiscuous humans only because the ensuing child survived to give rise to us and it is the human environment which has continued. The picture I have is that our Neanderthal genes today are due mostly to the Neanderthal females who were “impressed” into service by an aggressive and expanding human population. There may well have been Neanderthal male – human female offspring but they would more likely have been brought up in a Neanderthal environment, which – along with them -has not survived.
Ewen Callaway reports in Nature News:
Early European may have had Neanderthal great-great-grandparent
One of Europe’s earliest known humans had a close Neanderthal ancestor: perhaps as close as a great-great-grandparent.
The finding, announced on 8 May at the Biology of Genomes meeting in Cold Spring Harbor, New York, questions the idea that humans and Neanderthals interbred only in the Middle East, more than 50,000 years ago.
Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone’s genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).
……. All humans who trace their ancestry beyond sub-Saharan Africa carry a sliver of Neanderthal DNA — around 1–4% of their genomes. Researchers have long thought it most likely that early humans exiting Africa interbred with resident Neanderthals somewhere in the Middle East around 50,000—60,000 years ago, before travelling on to Asia, Europe and the rest of the world.
That possibility has gained support in the past year. Last year, a team that included Fu used the genome of a 45,000-year-old human from Siberia to date his Neanderthal ancestors to between 50,000 and 60,000 years ago (when modern humans were probably starting to leave Africa)2. Another reported finding the 55,000-year-old partial skull of a human in an Israeli cave not far from sites at which Neanderthals lived around the same time3.
But radiocarbon dating of remains from sites across the continent suggests that humans and Neanderthals lived together in Europe for up to 5,000 years in some areas — plenty of time for them to have met and interbred there, too.
But the AMH / Neanderthal co-existence was not a short-lived thing.
Encounters between AMH and Neanderthals probably took place at different times in different places to leave the genetic signal of some 3% Neanderthal genes in non-African AMH. Early encounters would have taken place in central Asia (perhaps 50,000 years ago) with later encounters in Europe (c. 30,000 years ago). Now new methods of radiocarbon dating at archaeological sites is providing evidence which indicates that Neanderthals and AMH overlapped for many hundreds of generations.
The k2p blog 
May 30, 2015 at 11:04 am
[…] females joined AMH bands as spoils of war. But only the offspring of the Neanderthal females have left their mark because they had joined the line that would […]