Abstract
The human Y chromosome exhibits surprisingly low levels of genetic diversity.
This could result from neutral processes if the effective population size of
males is reduced relative to females due to a higher variance in the number of
offspring from males than from females. Alternatively, selection acting on new
mutations, and affecting linked neutral sites, could reduce variability on the
Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and
mitochondrial DNA, in combination with extensive population genetic
simulations, we show that low observed Y chromosome variability is not
consistent with a purely neutral model. Instead, we show that models of
purifying selection are consistent with observed Y diversity. Further, the
number of sites estimated to be under purifying selection greatly exceeds the
number of Y-linked coding sites, suggesting the importance of the highly
repetitive ampliconic regions. Because the functional significance of the
ampliconic regions is poorly understood, our findings should motivate future
research in this area.
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