Human population history: a reconstruction based on HGDP genome-wide SNP data

From the press release:
'Our technique enables us to identify more subtle details about genetic contributions than other methods,' said Dr Garrett Hellenthal from the Department of Statistics at Oxford, a co-author on the paper. 'By incorporating the inheritance of 'blocks' of DNA between generations, rather than just individual genes, it captures a panoramic view of the sharing of patterns of DNA across the entire human genome. This allows us to consider a vast number of possible colonisation scenarios - not just the ones people have already thought of - and use an algorithm to determine the most likely migration routes.'

The new technique was used to analyse 2540 genetic markers using Single Nucleotide Polymorphism data from 927 individuals of diverse ethnicity whose DNA was collected by the Human Diversity Project.

'Humans like to tell stories and amongst the most captivating is the story of the global spread of modern humans from their original homeland in Africa,' said Dr Daniel Falush of University College Cork, a co-author on the paper. 'Traditionally this has been the preserve of anthropologists but geneticists are now starting to make an important contribution. However, genetic evidence is still typically analysed in the light of anthropological preconceptions; statistical techniques help us to see things more objectively.'

The researchers believe their method can cope with much larger datasets with over 500,000 genetic markers. Further developments of the technique should allow human ancestry to be reconstructed in unprecedented detail and give a perspective independent of anthropological theory and interpretation.

Sounds interesting, but no doubt far from definitive looking at only 2540 SNPs and a limited number of populations.
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.

[. . .]

Gene Flow from Europe to East Asia around the Arctic Circle

In our inferred scenario there is little gene flow between East Asian and Europeans and the Yakut is the only East Asian population to have two European donors; the Russians and the Orcadians. The Russian contribution is not surprising because the Yakut live in North East Russia. The Orcadian contribution is particularly noteworthy because removing these donors reduces the log-likelihood of generating the Yakut chromosomes by 2.5 times more than removing donors from any other population (Table S2). The Orcadians are also the only other European population to donate to other East Asians, namely the Han from Northern China and the Hezhen, who are also amongst the most Northerly East Asian populations in the sample. On this basis we hypothesize that there has been an episode of gene flow from Europe to East Asia. We tested the robustness of this inference by putting Orcadians last in the ordering. The Yakut replaced the Orcadians with Sardinians, who are a major donor to the Orcadians. The Hezhen and the Han from Northern China did not acquire new European donors, consistent with the gene flow from Europe being less quantitatively important to these two populations than to the more Northerly Yakut. Orcadians did not gain any East Asian donors by being placed last in the ordering, strengthening the inference that the direction of the gene flow was from Europe to East Asia.

Finns were not included in the analysis, but this independent evidence of west-east gene flow in northern Eurasia is in line with the theory that N3 (Tat C) Y chromosomes diffused from Northeastern Europeans to Siberians rather than the reverse:
The peculiar Y chromosomal DNA variant, known as Tat C, is also dominant in almost all the indigenous peoples of Siberia, from the nomadic Yakuts right across to the Chukchis and Siberian Inuits living on the shores of the Bering Strait - regardless of what language they may communicate in.

According to Prof. Villems, the "point" in all this is that among the Finno-Ugric races of Europe this genetic inheritance is much more diverse, more multibranched, and hence apparently older than among any of the Siberian peoples.

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