Tuesday, May 29, 2012
A genetic map of West Eurasia with a difference (aka. the ancestral dichotomy in our genomes)
What we have here is another genetic map of West Eurasia (Europe, West Asia and North Africa), using a new program and a few new samples. I usually employ the PLINK MDS utility to run such plots (see here), but this time I chose another algorithm which has just appeared online, called SPA. There are obviously some major differences between the SPA and PLINK maps, and the main one is that each subject appears twice on the SPA map.
That's because SPA offers a mode in which it assumes that the samples are of mixed ancestry, and divides their genomes into halves (represented by two sets of PC coordinates). One way to look at it is that each half represents a parent, but that would only be accurate for people who really are of mixed origin, with their parents coming from two clearly distinct groups in terms of genetic structure. So it's probably better to say that SPA turns each of the genomes into two of the most highly differentiated versions possible, across the first two dimensions. Also, as far as I can see, the program can come up with different solutions in different runs for the same person. Some of these solutions look like they're based on very ancient admixtures, and others more recent. In any case, I think this is an excellent way to show the dichotomy in our genetic data, even if we're not mixed.
The data sheet can be downloaded here, and run with programs like Gnuplot to make your own genetic maps. The map below was produced by me with Gnuplot, and then spruced up with color by Eurogenes project member FR7. A singe location version of the same plot, minus the color, can be seen here.
Wen-Yun Yang et al., A model-based approach for analysis of spatial structure in genetic data, Nature Genetics 44, 725–731 (2012), doi:10.1038/ng.2285