Modern Males Lack Neanderthal Y Chromosome Genes

Modern humans carry up to 4% Neanderthal DNA but a new paper reveals that the Neanderthal Y chromosome is distinct from any found in humans today. One would expect that since this ancient legacy of genomic DNA is present in modern day people it would also be present in the Y chromosome. Carlos Bustamante, from Stanford University in California, says,

“We’ve never observed the Neanderthal Y chromosome DNA in any human sample ever tested. That doesn’t prove it’s totally extinct, but it likely is.”

One possibility is that the Neanderthal Y chromosomes was initially circulating in the modern human gene pool, but were then lost by chance over the millennia. One other possibility is that female humans never mated with Neanderthal males. Another possibility is that they included genes that were incompatible with other genes found in modern humans. Indeed, the researchers found evidence to support this idea… Three are “minor histocompatibility antigens,” or H-Y genes, which resemble ones that transplant surgeons check to make sure that organ donors and organ recipients have similar immune profiles.


Because these Neanderthal genes are on the Y chromosome, they are specific to males. In theory, a female’s immune system might attack a male fetus carrying Neanderthal versions of these genes. If females consistently miscarried male babies carrying Neanderthal Y chromosomes, that would explain its absence in modern humans.

One thought on “Modern Males Lack Neanderthal Y Chromosome Genes

  1. I was reading on this also yesterday and had about the same headline as yours, what I found pretty much outraging, because we already knew so much. It is interesting that the Neanderthal Y-chromosome has been sequenced and the speculation about the possible reasons of its loss (same as for mtDNA anyhow, only an X-DNA lineage remains at low frequencies) but why that pointless headline: we already knew that from internal H. sapiens information, as the only possible “archaic” Y-DNA lineages exist in West Africa (where Neanderthal genetic legacy is negligible overall) and are too close to our own to be Neanderthal (much more likely to belong to some other proto-sapiens branch).

    Now, as for the speculation on the why the Neanderthal Y-DNA line didn’t survive, there is another even more powerful reason: only two or three sapiens Y-DNA lines (and two mtDNA ones) survive from that period among the OoA or “Greater Asian” macro-population (which is the one carrying Neanderthal genetics at low frequencies). With such a narrow founder bottleneck, the chances of any lineage representing a mere 2.5% of the ancestry to have survived the migration West Asia→India are effectively nil, no need to resort to incompatibility issues in fact: probability is enough.

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