Since the sequencing of the neandertal genome and subsequent additional archaic genomes, evidence of neandertal introgession (hybridization and backcrossing) has been found in nearly all non-african human genomes studied to date. For instance, I am ~2% neandertal and the distribution of neandertal alleles across current human genomes is scattered across all 22 autosomes. For instance, here are the neandertal markers detected across my genome (from 23andMe):
Late neandertal genomes (<50,000 years old) also have evidence of human introgression. When I teach about neanderthal ancestry in Evolutionary Biology, students often ask: “If neandertals and humans successfully mated, then aren’t we the same species?”. That, of course, all depends on your definition of “species”. Leaving that complex discussion aside, another fascinating observation from the analysis of archaic genomes has been that the neandertal contribution to the human genome has been found along all nuclear chromosomes except the Y (see my chromosomes above). This observation has been explained by a number a possibilities:
1. The Y chromosome is relatively small and any neandertal contributions to the human Y could have been lost by chance (genetic drift) over the last 40,000 or so years.
2. Natural selection could have maintained advantageous neandertal alleles and purified out deleterious ones, implying that Y-linked neandertal genes were BAD for H. sapiens.
3. Hybridization between human and neandertals may have only involved human males mating with neandertal females (“war brides”?).
4. Neandertal Y chromosomes may have been incompatible with human biology, or at least reduced the fertility of hybrid males with neanderthal fathers, due to significant divergence of the two species for over half a million years (neanderthal ancestors left Africa long before humans).
A new paper out takes a look at the neandertal Y chromsome and has some new evidence that supports number 4, and may also help us answer that species question as well, although none of the explanations above are completely mutually exclusive or inconsistent with available evidence. Interestingly, the authors find “missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens”, some of which are thought to “to elicit a maternal immune response during gestation”. In other words, male embyros with neandertal Y chromosomes may have ended in natural abortions at an early embryonic stage, making it impossible for Y-linked neandertal genes to accumulate in human populations. Under this scenario, female offspring of human-neandertal hybrids were viable, as were male hybrids with human fathers.