In the comments below a strange conversation grew out of the politicized nature of Pakistani identity, and its relationship to India the nation-state, and India the civilization. I assume that a typical reader, or more accurately commenter, on this weblog would be sanguine if they found out they were 10% chimpanzee. After all, it's what's between your ears that really matters, not who your ancestors were. I do understand that some readers have strong genealogical-nationalist interests in human population genetics, and that's fine so long as you don't presume that the rest of us share such priorities (this is a problem for some commenters, so please be aware that I get annoyed when you project this way, though it's obviously not a banning offense).
But readers who come via search engines are a different case, and that's why I've started to get worried about over-reading of PCA and such. Nevertheless, I do think PCA can answer the question of whether there is any real genetic discontinuity between Pakistanis and Indians. The answer is no. Page 19 of Reich et al. supplement 1 includes in the HGDP Pakistani populations in their plot of genetic variation of Indian groups. I've added some labels, but the top-line is rather clear. AP = Andhara Pradesh, UP = Uttar Pradesh, GUJ = Gujarat and RAJ = Rajasthan. I assume Ind. and Pak. abbreviations are self-evident.
Obviously it isn't strictly true that Pakistanis are just like Indians. But, Pakistanis are pretty much exactly where you'd expect from their position in relation to India. There is only a small component of recent Persian or Central Asian ancestry, as evident by the relative closeness of Muslim Pakistanis with Hindu groups, who would presumably lack this component. The point of this post isn't to vindicate or refute a particular political position, it's to reinforce what's been pretty clear from genetics over the past generation.
P.S. Just a small warning, if you leave a crazy comment, I'm not going to publish it!
