Wednesday, April 23, 2008

Do clines of genetic diversity say anything about migration patterns?

P-ter at GNXP discusses this Nature Genetics paper. The important point is that the maps of gradients of genetic similarity made famous by Cavalli-Sforza do not necessarily tell us anything about the pattern, direction, or speed of migrations of humans across continents.

Interpreting principal component analyses of spatial population genetic variation
John Novembre & Matthew Stephens
Nature Genetics Published online: 20 April 2008

Nearly 30 years ago, Cavalli-Sforza et al. pioneered the use of principal component analysis (PCA) in population genetics and used PCA to produce maps summarizing human genetic variation across continental regions1. They interpreted gradient and wave patterns in these maps as signatures of specific migration events1, 2, 3. These interpretations have been controversial4, 5, 6, 7, but influential8, and the use of PCA has become widespread in analysis of population genetics data9, 10, 11, 12, 13. However, the behavior of PCA for genetic data showing continuous spatial variation, such as might exist within human continental groups, has been less well characterized. Here, we find that gradients and waves observed in Cavalli-Sforza et al.'s maps resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns do not necessarily reflect specific migration events. Our findings aid interpretation of PCA results and suggest how PCA can help correct for continuous population structure in association studies.


morethangray said...

far out.

i found a link to this post on 'the dna network' rss, and am happy to see john getting some publicity on your blog.

Graham Coop said...

I've posted a comment on the article here

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