Researchers in Carlos Bustamante's lab at Stanford have recently compared the Y chromosomes of humans and Neandertals. They exome'd an exhumed 49k-year-old Neandertal male from El Sidron, Spain and found that his Y chromosome was not one that has been observed in modern humans. That is, his Y is likely extinct, gone from among the living.
About a month ago, I wrote about how the offspring of human and Neandertal matings couldn't have all been "mules" (couldn't have all been sterile), as some of us have Neandertal DNA in us. But what Bustamante's research reveals is that there were some male Neandertals who may not have mated successfully with humans (the success here being a fertile child), and they provide intriguing speculations about why.
Some of the genes on the Y chromosome can cause immune ruckus for the pregnant, whose male fetuses begin to express their male-specific histocompatibility genes. This can lead to miscarriages. Furthermore, (and equally fascinating) is that there are Neandertal and human-unique mutations on the Y chromosome in genes that are, in fact, histocompatibility genes. It's possible that these lineage-bound differences were incompatible with life when present in the fetuses of male human-Neandertals, perhaps explaining the absence of Neandertal Y in modern humans. As the authors muse, this is consistent with Haldane's rule: if one sex is absent, rare, or sterile among the the first generation matings of different groups, that sex is the heterogametic sex (the sex with the differing sex chromosomes; e.g. X/Y for males).
Mendez, F. L., Poznik, G. D., Castellano, S., & Bustamante, C. D. (2016). The Divergence of Neandertal and Modern Human Y Chromosomes. The American Journal of Human Genetics, 98(4), 728–734. doi:10.1016/j.ajhg.2016.02.023
I'm a Public Health Genetics PhD student at the University of Washington and a molecular epidemiology research fellow at the Fred Hutchinson Cancer Research Center. I post (mostly) about topics in epidemiology and genetics.