I do like to suggest that the genetic and archaeological record support the conjecture of Conan the Barbarian in terms of what our male ancestors thought was “good in life.” Basically, to conquer your enemies and seize their women, which is a distillation of a disputed quote from Genghis Khan. Conan may be fiction, but Genghis Khan is not. As it happens there is a fair amount of circumstantial evidence that the genetic legacy of Genghis Khan is enormous. Not only did Khan father many sons, but so did their sons, and so forth. Tens of millions of men around the world are direct paternal descendants of Genghis Khan and his family.
This is known. But now more is known, thanks to a new paper out of Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. The upside of this paper is that it uses whole genome sequence of Y chromosomes to generate phylogenetic inferences. This is important because the Y chromosome has very little genetic variation relative to much of the rest of the genome. The downside is that because techniques were utilized to perform whole genome sequencing of the Y, the sample size, at 299, is not as large as we’ve gotten used to for analyses of uniparental lineages. That will change in the future, as there are many thousands of whole genome sequences of the Y in databases around the world, though perhaps not enough computational power allocated by funding agencies to crunch through them in the fashion on display in the paper (they didn’t use the whole sequence for a lot of the analysis, but ~35,000 SNPs).
So what are the major findings of the paper? Using a Bayesian Skyline Plot (BSP) it is rather clear that 4-8 thousand years ago there was a sharp drop in male effective population sizes across many world populations. It is also clear that the female effective population did not experience the same drastic contraction. The supplements have individual figures, and many of the events of history and archaeology can be easily mapped onto these population size changes. For example, the later reduction of African population sizes probably is due to the later adoption of agriculture in that continent, and timed with the Bantu expansion. In the New World the data seem to show late and persistent reduction in effective population size. The Columbian Exchange and massive population contraction subsequent to that is probably being picked up by this result. 
Intriguingly there is a detection of a two events in the European data, where the sample size is relatively large. The first major drop seems to coincide with the arrival of the “First Farmers” (e.g., LBK culture) in Northern Europe. In the Middle East (orange) you see collapse, and then a rapid ascent very early. This comports well with the early history of agriculture here. But in the European samples there is a rapid ascent, and then a level off ~3,000 years ago or so. This could be the arrival of Indo-European cultures to Europe. If the sample sizes for other regions were as large and representative as Northern Europe such subtle details might also have emerged there with the BSP method (to be clear, I suspect the crash in effective size in Europe is due to haplogroup I, while the delayed expansion is due to R1a and R1b arriving a few thousand years later).
Also of interest are is the deep structure of the different clades. Those of you stepped in Y chromosomal haplogroups can extract more from the figure to the top left, but it shows relationship of the primary groups as well as their recent expansion. The affinity of the Q and R clades to me indicate that those who argue that these are somehow related to the “Ancestral North Eurasians” are correct. Similarly, the position of I and J in the same clade points to their common descent from ancient West Eurasian Pleistocene groups. The I lineage is most exclusively associated with European hunter-gatherers, while J is traditionally associated with groups of farmers expanding out of the Middle East in all directions (note that one branch of J is found in the Middle East, Central Asia, South Asia, and Europe). I agree with Dienekes that the branch of E that corresponds to the lineages which span Sub-Saharan Africa and Western Eurasia are a indicating a back migration to Africa, probably in the Pleistocene. I do wonder as well whether they have some association with the mysterious “Basal Eurasians.”
An important part of the paper that they emphasize is that ~50,000 years before the present there was a profusion of haplogroups associated with the ones which are today common across Eurasia, and Y chromosomal Ne was ~100. This seems to agree with the rapid expansion of non-Africans in the wake of the “Out of Africa” event, though the authors note they don’t have enough power to reject a model of a separate “Southern Route” migration, which might be detected with autosomal data. This is a good caution on the limitations of Y and mtDNA data; archaic admixture was rejected by these two loci because the non-African hominin lineages went extinct (mtDNA and Y have higher turnover rates than the recombining autosomal regions). 
Additionally there were some major lacunae in the sampling. For example, among the African populations it doesn’t seem like some of the hunter-gatherer groups, the Khoisan or eastern Pygmy, were included in the data set. The map also shows that Northeast Asia (China, Japan and Korea) and Oceania were not extensively sampled. But these are minor issues in the broader picture of the insights from the population coverage that they did have.
The most important implication of these sorts of results have to do with the nature of the change of human social organization and behavior over the course of the existence of modern humans. The authors of the above paper seem to understand this, as there is extensive focus on the topic within the paper:
An increase in male migration rate might reduce the male Ne but is unlikely to cause a brief drastic reduction in Ne as observed in our empirical data…However, in models with competition among demes, an increased level of variance in expected offspring number among demes can drastically decrease the N e (Whitlock and Barton 1997). The effect may be male-specific, for example, if competition is through a male-driven conquest. A historical example might be the Mongol expansions (Zerjal et al. 2003). Innovations in transportation technology (e.g., the invention of the wheel, horse and camel domestication, and open water sailing) might have contributed to this pattern. Likely, the effect we observe is due to a combination of culturally driven increased male variance in offspring number within demes and an increased male-specific variance among demes, perhaps enhanced by increased sex-biased migration patterns (Destro-Bisol et al. 2004; Skoglund et al. 2014) and male-specific cultural inheritance of fitness.
To restate what’s being said here:
1) During the Holocene we saw the rise of powerful patrilineages which engaged in winner-take-all of inter-group competition.
2) Within the “winning” patrilineages there may have been winner-take-all dynamics, or at least high reproductive variance
When it comes to farmers and nomads against each other I do think a model of inter-demic competition is pretty realistic. But when it comes to farmers and nomads against hunter-gatherers I don’t think one can term it competition. The latter in most circumstances would be quickly overwhelmed by the farmers and nomads; eliminated, excluded, or at least assimilated (there are exceptions in areas where the hunter-gatherer density was high and they were sedentary). And as concerns the complex societies of farmers and nomads, even within them the rise of inequality and stratification mean that subordinate or secondary males and their lineages were marginalized, leaving few descendants.
Men are on average 15-20 percent bigger than women. Men are also stronger than women. But the sexual dimorphism is far less than one can find among gorillas. This suggests that intra-sex competition among males was attenuated, or at least it was not in the physical domain. Though I am not of the camp which believes that war as we understand it must necessarily be a feature of Holocene agricultural societies, it seems likely that the pressure cooker of high population densities resulted in a radical increase in the scale of inter-group atrocity. One way to react to this change would have been to grow larger physically, but there are limitations to how fast biological evolution can resculpt the human physique. Not only that, but larger humans presumably require more nutritional inputs, and the agricultural revolution in Malthusian conditions did not enable that on a mass scale. So humans did what they do best: innovate culturally.
The cultural innovations came as package deals. A central role for patriarchal lineages which tended to apply force to maintain social order, as well as take on the position as the tip of the spear in inter-group competition, eventually resulted in power accruing to those groups almost exclusively. The importance of patrilineages naturally resulted in an increased importance of paternity certainty, and therefore social mores which emphasized female chastity. These powerful lineages fixed upon a solution which gorillas had long ago arrived at: treat females as chattel and defend them as one would property.
The “men in groups” were evoked by particular social-cultural conditions of agricultural society which they themselves did not necessarily trigger in an any way. But once you had a small benefit to the emergence of a caste of men in groups, groups which developed this caste benefited. Within these groups eventually the caste took over the identity of the group, and made its own interests conterminous with the interests of the group. The Athenian polis was democratic, but only for free males who were born of Athenians. In other words, the most radical experiment in radical democracy in the ancient world was also still relatively exclusionary and delimited in the nature of political power and representation (also, recall that the power of freeborn males of lower economic status in Athens has been connected to their importance in the navy as oarsmen).
Speaking as someone with broadly liberal sympathies, economic and social forces over the past few centuries have resulted in an unwinding of the cultural innovations of the past 10,000 years which have put a straight-jacket on the forces of human liberty. This great unwinding to some extent can be understood as the shattering of the great patriarchal monopolies of old, reflected in the great families and lineages which spanned the world, and democratic representation first for all men and then women. In the West the period between 1800 and 1970 saw massive gains in income to unskilled workers, reversing the tendency toward winner-take-all dynamics which arose with the Neolithic.
That being said, the post-Industrial and post-materialist world, in full flower in places like North Europe, is not exactly like the Paleolithic. Some of the innovations of the post-Neolithic world, such as organized religion, are probably here to stay in a world of social complexity and density. The great devolution to power from the elite male lineages is one specific aspect where I believe the modern age more resembles the Paleolithic. More liberal sexual ethics is also another dimension where the modern world is more like that of hunter-gatherers. But the autonomous individual, an island unto himself, is a fiction. Hunter-gatherers were, and are, social creatures. No doubt they were bound by taboos and rules, just as modern hunter-gatherers are. The vision of egalitarianism promoted by many in the modern West is a reaction against the social controls of the post-Neolithic world, but those social controls themselves are rooted in human cognitive impulses. Competition did not come full formed in the world of grain, and the impulse toward violence and domination was present in man long before the scythe was re-purposed toward bloodier ends.
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