In striking contrast to the mtDNA data, there is no strong evidence in Pakistani populations of Y-chromosome signatures of the early inhabitants of the region following the African exodus (Qamar et al. 2002, Zerjal et al. 2002), with their Y-chromosomes largely replaced by subsequent migrations or gene flow. The Y-chromosome gene pool of Pakistani populations is mainly attributable to western Eurasian lineages, particularly from the Middle East (Qamar et al. 2002). Conversely, few traces of East Asian haplogroups are observed in the Indus Valley populations. One Y-chromosome haplogroup (L-M20) has a high mean frequency of 14% in Pakistan and so differs from all other haplogroups in its frequency distribution. L-M20 is also observed, although at lower frequencies, in neighbouring countries, such as India, Tajikistan, Uzbekistan and Russia. Both the frequency distribution and estimated expansion time (7000 YBP) of this lineage suggest that its spread in the Indus Valley may be associated with the expansion of local farming groups during the Neolithic period (Qamar et al. 2002).
