This paper by Di Cristofaro et al. might well be the turning point in modern population genetics, at least as far as Eurasia is concerned anyway. Not only do the authors give up on the standard but dodgy method of dating Y-chromosome expansion times with Y-STR diversities, but they also conclude that, contrary to popular belief, Afghanistan and surrounds cannot be the source of any major population expansions into other parts of Eurasia. So this study really goes against the grain to what we've seen from academia in recent years, and I have to say it's very refreshing to finally read a paper like this which doesn't make the dubious claim that Y-chromosome haplogroup R1a is native to India.
Below are a few quotes and figure 2 from the study, showing the spatial distribution of six Ancestry Components (AC) from the K=9 ADMIXTURE analysis. Note the presence of the North European-specific AC4 in Central Asia, but almost complete lack of the South Asian-specific AC7 in Europe.
Given the uncertainties associated with Y-STR mutation rates  together with the onset of recent estimations of the Time to Most Recent Common Ancestor (TMRCA) of the various branching events in SNP based Y phylogenies using ‘complete’ Y sequences [74–76], in prudence, we choose not to estimate expansion times based on Y-STR diversities.
Our autosomal and haploid data suggested that the Afghan Hindu Kush populations exhibit a blend of components from Europe, the Caucasus, Middle East, East and South Asia. This juxtaposition of autosomal and haploid markers could reflect important male and female influences contributing to the Afghan populations’ genetic make-up. Considering autosomal data, all ancestral components displayed a decreasing gradient of their frequencies when approaching Afghanistan. Finding the highest genetic frequencies in a region does not necessarily mean that this region was the original source: it has been shown that geographic distributions can result from various modalities besides natural selection such as geographic barriers, subsequent migrations, replacement, isolation, and the surfing effect . However, the fact that all the ancestral components reach a lower frequency when in Afghanistan supports the model of a convergence of migrations [87,88].
Although the modern Afghan population is made up of ethnically and linguistically diverse groups, the similarity of the underlying gene pool and its underlying gene flows from West and East Eurasia and from South Asia is consistent with prehistoric post-glacial expansions, such as an eastward migration of humans out of the Fertile Crescent in the early Neolithic period, and the arrival of northern steppe nomads speaking the Indo-Iranian variety of Indo-European languages. Taken together, these events led to the creation of a common genetic substratum that has been veneered with relatively recent cultural and linguistic differences.
Di Cristofaro J, Pennarun E, Mazie`res S, Myres NM, Lin AA, et al. (2013) Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge. PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748