Population Genetics
The Y chromosome, as has been stated above, is passed from father to son directly with minimal genetic re-combination. Therefore a sons Y-chromosome will be identical to his fathers and his grandfather etc. etc.
Therefore a view of inheritance can be built up by looking at the non-recombining section of the Y-chromosome.
This can be used in the same way as mtDNa because like mitochondria, there is no recombination between generations. It also gives the other half of the story i.e. tracing the paternal line (maternal lines have been studied much more extensively up to the present date).
The main advantages of this approach are that the Y-chromosome is much larger than mitochondrial DNA, and has a slower mutation rate. This allows the analysis of very deep branches (in time) with relative accuracy, which may not be present in mtDNA analysis due to reverse mutations leading from the higher mutation rate present in mtDNA.
The resolution of detail within the y-chromosome has recently been greatly improved by the introduction of denaturing high-performance liquid chromatography (Richards + Macaulay, 2001), which also increases its expense.
Future work in to population genetics is likely to comprise mainly of Y-chromosome studies, due to a lack of past work. This is mainly due to the ease of mtDNA analysis compared to Y-chromosome analysis, but now the gaps of knowledge left must be filled.