Arguably the most important cultural transition in the history of modern humans was the development of farming, since it heralded the population growth that culminated in our current massive population size. The genetic diversity of modern populations retains the traces of such past events, and can therefore be studied to illuminate the demographic processes involved in past events. Much debate has focused on the origins of agriculture in Europe some 10,000 years ago, and in particular whether its westerly spread from the Near East was driven by farmers themselves migrating, or by the transmission of ideas and technologies to indigenous hunter-gatherers. This study examines the diversity of the paternally inherited Y chromosome, focusing on the commonest lineage in Europe. The distribution of this lineage, the diversity within it, and estimates of its age all suggest that it spread with farming from the Near East. Taken with evidence on the origins of other lineages, this indicates that most European Y chromosomes descend from Near Eastern farmers. In contrast, most maternal lineages descend from hunter-gatherers, suggesting a reproductive advantage for farming males over indigenous hunter-gatherer males during the cultural transition from hunting-gathering to farming.I think the discrepancy between the male and female lineages is a sign that we don't understand this data very well. This would be like finding out that contemporary Americans are mostly descended from Europeans in the male lineage and American Indians in the female lineage. We have no evidence the men in the European neolithic had multiple wives, and everything we know about primitive farmers worldwide suggests that this is unlikely. What we know about the interactions between neolithic farmers and mesolithic hunters in Europe (not much, admittedly) does not suggest intermarriage or any other form of close cultural contact.
One day we may understand this data well enough to make some statements about history based on it, but that appears to still be a ways in the future.