As I have mentioned in a previous entry, the genetic structure of human populations has been interpreted as the result of a process of "serial bottlenecks", starting from the major "Out of Africa" bottleneck, and followed by a series of other ones, as humans colonized the world. Bottlenecks reduce genetic diversity, but so does selection, and it is imperative to directly sample genetic diversity of past populations, to see how well they conform with the expectations of the "serial bottlenecks" theory, i.e., whether reduced diversity is due to descent from a few individuals whose progeny transcended the bottleneck, or due to selection, which suppresses genetic variation by removing some alleles from the gene pool.
This paper argues in favor of selection as a mechanism for keeping genetic diversity (and hence effective population size) at low levels. This selection process, is not, however, envisioned as affecting the species as a whole, but rather proceeded in its own way in regional subsets of humans. These groups did not exchange genes randomly with other such groups, but rather according to their degree of cultural similarity.
John Hawks has an extensive post on this article, which I recommend.
Culture, population structure, and low genetic diversity in Pleistocene hominins
L.S. Premo, Jean-Jacques Hublin
Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.