A somewhat technical yet interesting study on Y chromosome evolution in humans:
Melissa A. Wilson Sayres et al., Natural Selection Reduced Diversity on Human Y Chromosomes. PLoS ONE 2014. Open access → LINK [doi:10.1371/journal.pgen.1004064]
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.
Positive selection (or directional selection) happens when a variant gets so good that everything else becomes bad by comparison. This may be just because an environmental change, possibly caused by migration (or whatever other reason) substantially alters the rules of the game. Much more rarely a novel mutation (or accumulation of several of them) may happen to generate a phenotype that is much more fit even for pre-existent conditions. As I understand it, positive selection does happen only rarely (but spectacularly). An example in humans is the selection of whiter skin shades in latitudes far away from the tropics (because of the "photosynthesis" of vitamin D in the skin, crucial for early brain development), another more generalized one is the selection for improved brains (not necessarily just bigger), able to face changing conditions more dynamically and develop more efficient tools and weapons.
Purifying selection (or negative selection) is quite different and surely much more common. As novel mutations arise randomly, in at least many cases, the vast majority I dare say, they happen to be harmful for a previously well-tuned genotype (and its derived phenotype). As result, the carriers have decreased opportunities for reproduction, when they don't just die right away. Natural selection acts mostly this way and in many cases the types can become very stable for this reason, as happens with genera that have been successful on this planet since long before humankind arose, such as sharks or crocodiles.
This last is what seems to be happening to the human Y chromosome: novel mutations are at least quite often harmful (maybe they cause sterility or whatever other traits in the male that cause decreased reproductive efficiency) and they are regularly pruned off the tree by natural selection.
Purifying selection slows down the effective mutation rate
Interestingly the authors mention that:
... if purifying selection is the dominant force on the Y chromosome, the topology of the tree should remain intact, but the coalescent times are expected to be reduced.
That would be, I understand, because the observed mutation rate has little relation with the actual accumulated (effective) mutation rate, which is much slower because of the continuous pruning of the negative selection.
Purifying selection has also been observed in the mitochondrial DNA, having the same kind of slowing impact on the "molecular clock".