One potential avenue for extending the current approach to achieve this goal would be to impute chromosomes from “ancestral populations,” which would both represent populations that existed in the past and also act as efficient donors for the modern haplotypes.Rather than seeing human variation as a network of gene exchange between the sampled populations, the goal should be to create a rich history of mankind where the named identifiable present-day populations are seen as leaves of a hidden web of interconnections between inferred, but statistically sound past populations, which in turn would be mapped to historical-archaeological entities.
PLoS Genet 4(5): e1000078. doi:10.1371/journal.pgen.1000078
Inferring Human Colonization History Using a Copying Model
Garrett Hellenthal et al.
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 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.