Where Did The Neanderthal Y Chromosome Go?

Missing Y chromosome kept us apart from Neanderthals | New Scientist

There is no serious doubt outside creationist circles these days that a) modern humans and Neanderthals were different species of human who lived contemporaneously in Eurasia, and b) they interbred very occasionally but not often and not very successfully.

Neanderthal DNA has been identified in non-African modern humans, mostly on the X chromosome. It has been associated with pale skin and other cold-climate adaptations but also with arthritis, auto-immune conditions, depression and even addiction.

But there was one little problem. Had we got our Neanderthal genes from male Neanderthals we should expect to see some modern males with Neanderthal Y chromosomes. Because the Y chromosome doesn't pair up and exchange information with another chromosome during formation of gametes there would be nothing to dilute the Neanderthal DNA on a Y chromosome with modern human DNA. We would expect a little mutation here and there over the intervening years but any inherited Neanderthal Y chromosomes should be easily recognisable as substantially different to the normal Homo sapiens Y chromosomes.

The problem is, none has ever been found.

Now a team of researchers from Stamford University, Stamford, CA, USA believe they have found the reason. Their findings are presented open-access in The American Journal of Human Genetics:

Abstract
Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

The Divergence of Neandertal and Modern Human Y Chromosomes
Mendez, Fernando L. et al.
The American Journal of Human Genetics , Volume 98 , Issue 4 , 728 - 734 DOI: 10.1016/j.ajhg.2016.02.023

© 2016 The Authors. Published by Elsevier Inc. Reprinted under terms of Creative Commons Attribution License (CC BY 4.0)

It is possible that the number of matings was so small that the Neanderthal Y chromosome in modern humans simply drifted to extinction but it seems more likely that there was something else going on. It seems from this team's findings that the Neanderthal Y chromosome had diverged so far from that of H. sapiens that it was positively harmful in a H. sapiens embryo. In particular some of the difference, when found as mutations in H. sapiens Y chromosomes are single point mutations that cause a histocompatibility mismatch between the embryo and the mother, causing a maternal immune response to kill the embryo.

It seems likely then that the reason we see no Neanderthal Y chromosomes today is because they didn't survive in modern humans.

What we have here is a good example of two sister species having diverged far enough to be regarded as two distinct species but which retained the ability to hybridize infrequently and not very successfully. However, some of the few genes that did cross the species barrier were so beneficial to the Eurasian population that they spread quickly pulling some less beneficial ones with them.

I wonder if a creationist 'expert' on human evolution could tell me where a notion about an original founder couple fits these known facts. Clearly, non-African humans are the result of a hybridization between three different species (including Denisovans) which had diverged over a long period before coming back into contact.

Incidentally, for those creationists who believe the Theory of Evolution is a theory in crisis and will only last a few more years, just as they have been predicting for the last 60 years or more, perhaps they would like to re-read the above Abstract to see how this entire paper only makes sense in terms of evolution and how validity of the theory is taken completely for granted.

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