@article {308286,
	title = {The Divergence of Neandertal and Modern Human Y Chromosomes.},
	journal = {Am J Hum Genet},
	volume = {98},
	year = {2016},
	month = {2016 Apr 7},
	pages = {728-34},
	abstract = {<p>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 Sidr{\'o}n, 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\&nbsp;chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is\&nbsp;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.</p>
},
	issn = {1537-6605},
	doi = {10.1016/j.ajhg.2016.02.023},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/27058445},
	author = {Mendez, Fernando L and Poznik, G David and Castellano, Sergi and Bustamante, Carlos D}
}
