Tuesday, May 29, 2012
A genetic map of West Eurasia with a difference (aka. the ancestral dichotomy in our genomes)
I've mostly been using the PLINK MDS utility to produce genetic maps up to this point, but today I chose another algorithm called Spatial Ancestry analysis (SPA). It's just appeared online, and seems to be a lot faster than PLINK, but with comparable results.
Also, SPA offers an option to split genomes into halves, by providing two sets of PC coordinates for each individual. One way to look at it is that each half represents a parent, but that's usually only accurate for people who really are of first-generation mixed origin. So it's probably better to say that SPA turns the samples into two of the most genetically differentiated versions possible. Moreover, as far as I can see, the program can come up with different solutions in different runs for the same person, and some of these solutions appear to be based on very ancient admixtures. In any case, I think this is an excellent way of showing the dichotomy in our genetic structure, even if we're not recently 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