  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. While we show that purifying selection removing
deleterious mutations can explain the low diversity on the Y chromosome, we
cannot exclude the possibility that positive selection acting on beneficial
mutations could have also reduced diversity in linked neutral regions, and may
have contributed to lowering human Y chromosome diversity. Because the
functional significance of the ampliconic regions is poorly understood, our
findings should motivate future research in this area.
