The Divergence of Neandertal and Modern Human Y Chromosomes
Fernando L. Mendez correspondence email, G. David Poznik, Sergi Castellano, Carlos D. Bustamante correspondence email
Open Access
Publication History Published: April 7, 2016 Accepted: February 26, 2016 Received: December 22, 2015
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Creative Commons Attribution (CC BY 4.0)
Relationship of Neandertal Y Chromosome to Those of Modern Humans
The genealogy (red tree) can be parsimoniously explained as mirroring the population divergence (gray tree). We find no evidence for (a) a highly divergent super-archaic origin of the Neandertal Y chromosome, (b) ancient gene flow post-dating the population split, or (c) relatively recent introgression of a modern human Y chromosome into the Neandertal population.
Summary
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.
Received: December 22, 2015; Accepted: February 26, 2016; Published: April 7, 2016
© 2016 The Authors. Published by Elsevier Inc.
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