  The paternally inherited Y chromosome has been widely used in population
genetic studies to understand relationships among human populations. Our
interpretation of Y chromosomal evidence about population history and genetics
has rested on the assumption that all the Y chromosomal markers in the
male-specific region (MSY) are selectively neutral. However, the very low
diversity of Y chromosome has drawn a long debate about whether natural
selection has affected this chromosome or not. In recent several years, the
progress in Y chromosome sequencing has helped to address this dispute.
Purifying selection has been detected in the X-degenerate genes of human Y
chromosomes and positive selection might also have an influence in the
evolution of testis-related genes in the ampliconic regions. Those new findings
remind us to take the effect of natural selection into account when we use Y
chromosome in population genetic studies.
