Garrett Hellenthal and colleagues (2008)

Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single "Out-of-Africa" bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native South Americans have received ancestry from a source closely related to modern North-East [sic] Asians (Mongolians and Oroquen) that is distinct from the sources for native North Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form.

One aspect of the paper is that the authors document a diversity cline (gradient of genetic variation) going from high diversity in and near Africa to lower diversity far from Africa. This observation is not new -- it has been made many times previously, on the basis of SNP variation, STR variation, mitochondrial DNA variation, and craniometric variation.

This observation has often been interpreted as evidence for a large-scale out-of-Africa migration. The reason for the cline would be the successive founding of populations: one group of migrants leaves Africa with a subset of African genes, then that population divides and a subset of people go farther along, and so forth.

I have criticized this interpretation before. To be sure, serial founder effects are a possible interpretation of the diversity cline.

In my opinion, there is a serious drawback to interpreting autosomal variation as a result of successive founder events. A large fraction of the autosomal genome has recently been subject to positive selection. Positive selection is certainly the most potent reason why we might see long-distance movement of "portions of chromosomes" -- the selected allele itself and a long chromosomal region hitchhiking along with it will be at elevated frequencies across a broad geographic area.

But the text of the paper includes no mention of natural selection. It is understandable why one might like to ignore selection, since it makes everything easier if selection never happens. The model in the paper assumes that drift and migration are the only factors affecting these gene regions. Since they are using someone else's data, they may find it difficult to sort out where selection may have been important.

But the reality is that

Given that, I don't think that the regions sampled in this paper have the power to resolve ancient population movements, as distinct from occasional long-distance gene flow. In other words, we aren't necessarily looking at bottlenecks, founder events, and mass migrations -- we may instead be looking at an occasional traveler along the Silk Road.

References:

Hellenthal G, Auton A, Falush D. 2008. Inferring Human Colonization History Using a Copying Model. PLoS Genet 4(5): e1000078. doi:10.1371/journal.pgen.1000078