For millions of years it was believed that the human Y chromosome is a stagnant part of human genome and is degrading constantly having lost 1,393 of its 1,438 original genes over the course of its existence. With a rate of genetic loss of 4.6 genes per million years, the Y chromosome was believed to potentially lose complete function within the next 10 million years. Comparative genomic analysis revealed that many mammalian species are experiencing a similar loss of function in their heterozygous sex chromosome. Degeneration was believed to be the fate of all nonrecombining sex chromosomes due to three common evolutionary forces: high mutation rate, inefficient selection and genetic drift. The human Y chromosome is particularly exposed to high mutation rates due to the environment that it is housed in. The Y chromosome is passed exclusively through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a risk of mutation 4.8 times greater than the rest of the genome.
Some facts about the Y chromosome.
The Y chromosome is the one of the two sex-determining chromosomes in most mammals, including humans. Most mammals have one pair of sex chromosomes in each cell. Males have one Y chromosome and one X chromosome, while females have two X chromosomes
Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. The Y chromosome likely contains between 70 and 200 genes. Because only males have the Y chromosome, the genes on this chromosome tend to be involved in male sex determination and development. Sex is determined by the SRY gene, which is responsible for the development of a fetus into a male. Other genes on the Y chromosome are needed for normal sperm production important in male fertility. The human Y chromosome is composed of about 60 million base pair and represents approximately 2% of the total DNA in the cell. Genes on the Y chromosome are among the estimated 20,000 to 25,000 total genes in the human genome.
Contrary to the presently held belief, researchers at the Whitehead Institute for Biomedical Research at MIT in Cambridge through their studies have been able to demonstrate that the human Y chromosomes are not degrading, in fact they are evolving at a high rate. Researcher David Page of MIT, who first sequenced the human Y chromosomes in 2003 
has also been successful now in completely sequencing the Y chromosome of the closest relative of humans-the chimpanzee. Comparison of the human and chimpanzee Y chromosomes revealed unexpected results. Since human and chimp DNA generally differ by less than 2 per cent, scientists expected the two sequences to look very similar but surprisingly found more than 30 per cent of the Y chromosome differed between the two species.This is a direct evidence that the human Y chromosome is evolving rapidly and dynamically. The region of the Y chromosome that is involved in sperm production was found to be evolving at a fast pace whereas the rest of the regions were evolving only a bit faster than the rest of the genome. Several factors probably account for the rapid evolution of the Y chromosome. First, the trick it uses to repair genes — known as gene conversion — is probably less efficient than the repair mechanisms used elsewhere in the genome. This allows new mutations to arise more often.These mutations are then subject to greater selective pressure than the rest of the genome — because of the important role of the Y chromosome in sperm production. Any advantageous mutations would be expected to be preserved as they boost fertility, while deleterious ones would be rapidly flushed from the gene pool. The scientists also suspect that the rapid divergence of the Y chromosome from the common ancestor of humans and chimpanzees may be due to differences in mating behaviour.In chimpanzees, multiple males may mate with a female one after the other, resulting in intense competition among the sperm to fertilize the egg.If a chimp produces more sperm, it’s more likely that its sperm will fertilize the egg and pass its genes on to the next generation.
On the whole this latest research from Massachusetts Institute of Technology shows that we are still far from completely understanding the true facts about the male Y chromosome.