“Why is there no Neanderthal y-DNA in modern humans?”

My theory is very simple:

All Neanderthal males were killed and the females mated with. Over a period of thousands of years that is. Neanderthals lived in small groups of around 30. There were around 30,000 Neanderthals in total during the time Homo sapiens began to enter Europe. That would mean that there were around 1,000 Neanderthal groups spread all over Europe and some Asia.

Homo sapiens likely entered the regions in large groups of males. Groups of 30 Neanderthals had maybe 5-8 adult males of “fighting age” meaning not children and not seniors.

They were easily outnumbered and probably surprised by the invasions. They didn’t prepare for what they didn’t see coming. Similar to the Basques who later would experience something similar.

The claim has been made that there was incompatibility and Neanderthal men couldn’t have gotten sapiens women pregnant, but I strongly doubt that the Neanderthal men ever had a chance to mate with sapiens women.

Maciamo takes on the subject on Eupedia:

“Very interesting, but I have serious doubts about antigens eliciting a maternal immune response during gestation. Half a million year of divergent evolution is not enough to bring to related sub-species to the limit of biological compatibility. The evidence for that is that lions and tigers can procreate and give birth to both male and female fertile offspring (tigons or ligers, depending if the father is a tiger or a lion), even though their common ancestors lived 3.5 million years ago. The same is true for dogs, wolves, coyotes, jackals and perhaps also foxes (see canine hybrids, e.g. the coywolf), and canidae branched off from one another even longer ago, approximately 12 million years ago (7.5 million if we exclude foxes).

The only reason that a mule is infertile is that horses and donkeys don’t have the same number of chromosomes (like humans and chimpanzees). So far all evidence suggest that Neanderthals and Denisovans had 23 pairs of chromosomes like Homo sapiens, and indeed if they didn’t we wouldn’t carry traces of their DNA today (as hybrids would have been infertile).

Additionally, the severe population bottleneck in the genus Homo caused Y-chromosomes to be very similar to one another compared to chimpanzee Y-chromosomes. In other terms, when compared to two chimpanzees belong to very distant Y-haplogroups, Homo sapiens and Neanderthal Y-DNA look very similar. There is no rational reason to believe that this would have caused an immune reaction leading to miscarriage.”

Source: Neanderthal Ydna

As for the claim that it could have been Rhesus or ABO incompatibility with Neanderthal men being Rh positive and sapiens women Rh negative:

The other way around seems more plausible. The “Cro-Magnons” came from Africa where Rh negative blood is relatively low and the Neanderthals are natives to Europe where the percentage of Rh negative blood is still relatively high.

The Neanderthals examined in Spain were found to have blood type O (Rh factor not determined) meaning ABO incompatibility would have also been unlikely.

What were the blood types of the Neanderthals?

As for mtDNA:

“Why are there no Neanderthal mtDNA haplogroups present in modern humans?”

See also:

Why did the Neanderthals go extinct?