May 30, 2012

Spatial Ancestry Analysis (Yang et al. 2012)

Link to SPA software.

Nature Genetics 44, 725–731 (2012) doi:10.1038/ng.2285

A model-based approach for analysis of spatial structure in genetic data

Wen-Yun Yang et al.

Characterizing genetic diversity within and between populations has broad applications in studies of human disease and evolution. We propose a new approach, spatial ancestry analysis, for the modeling of genotypes in two- or three-dimensional space. In spatial ancestry analysis (SPA), we explicitly model the spatial distribution of each SNP by assigning an allele frequency as a continuous function in geographic space. We show that the explicit modeling of the allele frequency allows individuals to be localized on the map on the basis of their genetic information alone. We apply our SPA method to a European and a worldwide population genetic variation data set and identify SNPs showing large gradients in allele frequency, and we suggest these as candidate regions under selection. These regions include SNPs in the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B.

Link

8 comments:

  1. princenuadhaWednesday, May 30, 2012 7:37:00 am

    Wow, the Swiss Germans almost completely overlap with the Germans.

    ReplyDelete
  2. pconroyWednesday, May 30, 2012 10:58:00 pm

    The map in the supplementary material is similar to one I saw a few years ago. All Europe countries seem to map correctly, except for:

    1. Slovakia - near Cyprus
    2. Latvia - far to the North East, where Northern Russia should be.

    ReplyDelete
  3. eurologistThursday, May 31, 2012 12:17:00 pm

    If you look at Germany, it is exactly what you would expect from it's location and diffusion, and you can actually clearly see all of this when you travel it. Many far northern Germans look like Danes and Swedes, NW Germans like the adjacent Dutch (they even speak a mutually intelligible language). There is a hole with Belgium (boarder Germans look nothing like them - as also evident here), but of course continuation in the Alsace region and then in the general Alemann areas, and further into Austria.

    The overlap then continues along the Danube corridor with Czech and Hungarian, and further north with Poland - which was mostly Germanic until Slavic expansion ~1,500 years ago.

    Of further interest are the "cis-alpine" French in Italy, and the likely Etruscan Swiss. I am not at all surprised by the Latvian placement.

    ReplyDelete
  4. princenuadhaFriday, June 01, 2012 8:36:00 pm

    Ya, its essentially the same map. You can tell for sure by the outliers.

    One important difference is that S. Italy and S. Balkans have sifted eastward, and dragged the cline in that direction too. Another change is that the sardinians are now east of Spaniards.

    I don't know what the researchers are doing but my guess is that they want to recreate a map of Europe.

    ReplyDelete
  5. Average JoeMonday, June 04, 2012 12:30:00 am

    Dienekes:

    How you read this paper yet? What do you think of it?

    http://www.scirp.org/journal/PaperInformation.aspx?paperID=19566

    ReplyDelete
  6. DienekesMonday, June 04, 2012 12:37:00 am

    It's not worth a damn.

    ReplyDelete
  7. princenuadhaMonday, June 04, 2012 6:47:00 am

    "It's not worth a damn."

    Lol. Is it just that article that's bad or is the whole journal and publishing group that sucks?

    Did you see that r1b paper from the same journal. It seemed pretty odd to me.

    ReplyDelete
  8. princenuadhaFriday, June 08, 2012 6:11:00 am

    Dienekes, how come you never posted this study from 2010?

    http://www.nature.com/hdy/journal/v106/n1/abs/hdy201047a.html

    ReplyDelete

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