SUMMARY Although hominins were present in Europe as early as ~780 thousand years ago, there is broad agreement that these archaic humans, including Neanderthals, contributed little to the contemporary European gene pool. In contrast, there is vigorous debate about the relative contributions of humans who entered in the Upper Paleolithic and Neolithic. Here, we argue that the Y-chromosomal diversity pattern is likely to have a largely Neolithic or later origin. In addition to the genome-wide influences resulting from migration, admixture and drift, the effects of positive selection are detectable around some genes, such as lactase. Studies of species associated with humans, e.g. cattle, are providing additional insights.